Data Structures
struct	KSEPI_SEQUENCE

struct	KSEPI_FLEET_SEQUENCE

Macros
#define	KSEPI_MINHNOVER 8 /* N.B. overscans below about 16-24 should be avoided for long TE */

#define	KSEPI_MAXRBW_NORAMPSAMPLING 125.0

#define	KSEPI_DEFAULT_SSI_TIME_ICEHARDWARE 100

#define	KSEPI_DEFAULT_SSI_TIME 1500

#define	KSEPI_INIT_SEQUENCE1 KS_INIT_SEQ_CONTROL, KS_INIT_EPI, KS_INIT_EPI, KS_INIT_TRAP, KS_INIT_SELRF, KS_INIT_SELRF, KS_INIT_SELRF, KS_INIT_TRAP, KS_INIT_TRAP, KS_INIT_WAIT, KS_INIT_WAIT

#define	KSEPI_INIT_SEQUENCE2 KS_INIT_TRAP, KS_INIT_TRAP, KS_INIT_PHASEENCODING_PLAN, KS_INIT_PHASEENCODING_PLAN, KS_INIT_PHASEENCODING_PLAN, NULL

#define	KSEPI_INIT_SEQUENCE {KSEPI_INIT_SEQUENCE1, KSEPI_INIT_SEQUENCE2};

#define	KSEPI_FLEET_INIT_SEQUENCE {KS_INIT_SEQ_CONTROL, KS_INIT_EPI, KS_INIT_TRAP, KS_INIT_SELRF, KS_INIT_WAIT, KS_INIT_WAIT, KS_INIT_PHASEENCODING_PLAN};

#define	MAX_DIFSCHEME_LENGTH 1024

Typedefs
typedef float	DIFFSCHEME[3][MAX_DIFSCHEME_LENGTH]

Enumerations
enum	KSEPI_MULTISHOT_MODE { KSEPI_MULTISHOT_OFF, KSEPI_MULTISHOT_ALLVOLS, KSEPI_MULTISHOT_1STVOL, KSEPI_MULTISHOT_B0VOLS }

enum	OFFLINE_DIFFRETURN_MODE { OFFLINE_DIFFRETURN_ALL = 0, OFFLINE_DIFFRETURN_ACQUIRED = 1, OFFLINE_DIFFRETURN_B0 = 2, OFFLINE_DIFFRETURN_MEANDWI = 4, OFFLINE_DIFFRETURN_MEANADC = 8, OFFLINE_DIFFRETURN_EXPATT = 16, OFFLINE_DIFFRETURN_FA = 32, OFFLINE_DIFFRETURN_CFA = 64 }

Functions
STATUS	cvinit (void)

STATUS	cveval (void)

STATUS	my_cveval (void)

STATUS	cvcheck (void)

STATUS	predownload (void)

STATUS	pulsegen (void)

STATUS	mps2 (void)

STATUS	aps2 (void)

STATUS	scan (void)

	abstract ("EPI [KSFoundation]")

	psdname ("ksepi")

STATUS	ksepi_eval_flowcomp_phase (KS_TRAP fcphase, const KS_EPI epi, const char *desc)

STATUS	ksepi_pg (int start_time)

int	ksepi_scan_coreslice (const SCAN_INFO *slice_pos, int dabslice, int shot)

int	ksepi_scan_coreslice_nargs (const SCAN_INFO slice_pos, int dabslice, int nargs, void *args)

int	ksepi_scan_sliceloop (int slperpass, int volindx, int passindx, int shot)

int	ksepi_scan_sliceloop_nargs (int slperpass, int nargs, void **args)

STATUS	ksepi_scan_seqstate (SCAN_INFO slice_info, int shot)

float	ksepi_scan_acqloop (int passindx, int volindx, int multishotflag)

float	ksepi_scan_scanloop ()

void	ksepi_init_imagingoptions (void)

STATUS	ksepi_init_UI (void)

STATUS	ksepi_eval_UI ()

STATUS	ksepi_eval_setuprf_3dexc (KS_SELRF *selrfexc, int rf3Dopt)

STATUS	ksepi_eval_setuprf ()

STATUS	ksepi_eval_setupfleet ()

STATUS	ksepi_eval_setupobjects ()

STATUS	ksepi_eval_TErange ()

STATUS	ksepi_eval_inversion (KS_SEQ_COLLECTION *seqcollection)

STATUS	ksepi_eval_tr (KS_SEQ_COLLECTION *seqcollection)

int	ksepi_eval_ssitime ()

STATUS	ksepi_eval_scantime ()

STATUS	ksepi_check ()

STATUS	ksepi_predownload_plot (KS_SEQ_COLLECTION *seqcollection)

STATUS	ksepi_predownload_setrecon ()

STATUS	ksepi_pg_fleet (int start_time)

STATUS	ksepi_fleet_scan_seqstate (const SCAN_INFO *slice_info, int shot)

void	ksepi_scan_rf_off ()

int	ksepi_fleet_scan_coreslice (const SCAN_INFO *slice_pos, int dabslice, int shot)

int	ksepi_fleet_scan_sliceloop (int slperpass, int volindx, int passindx)

STATUS	ksepi_scan_init (void)

STATUS	ksepi_scan_prescanloop (int nloops, int dda)

STATUS	ksepi_diffusion_readtensorfile (DIFFSCHEME diffscheme, int nb0, int ndirs)

float	ksepi_diffusion_getmaxb ()

void	ksepi_diffusion_set_heat_scaling (DIFFSCHEME diffscheme)

STATUS	ksepi_diffusion_init_UI ()

STATUS	ksepi_diffusion_eval_UI ()

void	SolveCubic (double a, double b, double c, double d, int nsol, double x)

STATUS	ksepi_diffusion_calcTE (double *TE_s, int exciso2end, int crsh1_half180, int half180_crsh2, int crsh3_half180, int half180_crsh4, int readout2echo, int ramptime, float G, int bval_desired, int dualspinechoflag)

STATUS	ksepi_diffusion_eval_gradients_TE (KSEPI_SEQUENCE *ksepi)

STATUS	ksepi_diffusion_predownload_setrecon ()

STATUS	ksepi_diffusion_pg (KSEPI_SEQUENCE *ksepi, int TE)

void	ksepi_diffusion_scan_diffamp (KSEPI_SEQUENCE *ksepi, int volindx)

Variables
KS_SEQ_COLLECTION	seqcollection

float	ksepi_excthickness = 0

float	ksepi_gscalerfexc = 0.9 with {0.1, 3.0, 0.9, VIS, "Excitation slice thk scaling (< 1.0 thicker slice)",}

int	ksepi_slicecheck = 0 with {0, 1, 0, VIS, "move readout to z axis for slice thickness test",}

float	ksepi_spoilerarea = 3000.0 with {0.0, 10000.0, 3000.0, VIS, "ksepi ksepi.spoiler gradient area",}

int	ksepi_rfspoiling = 1 with {0, 1, 1, VIS, "Enable RF spoiling 1:on 0:off",}

int	ksepi_fse90 = 0 with {0, 1, 0, VIS, "Use FSE90 instead of SPSP for non-fatsat",}

int	ksepi_rf3Dopt = 0 with {0, 10, 0, VIS, "Choose optimized SPSP pulse for 3D [0:OFF]",}

float	ksepi_kissoff_factor = 0.04 with {0, 1, 0.04, VIS, "Slice oversampling fraction on each side (3D)",}

float	ksepi_crusherscale = 1.0 with { -20.0, 20.0, 1.0, VIS, "scaling of crusher gradient area",}

float	ksepi_gscalerfref = 0.9 with {0.1, 3.0, 0.9, VIS, "Refocusing slice thk scaling (< 1.0 thicker slice)",}

int	ksepi_rampsampling = 1 with {0, 1, 1, VIS, "Rampsampling [0:OFF 1:ON]",}

int	ksepi_readlobegap = 0 with {0, 10ms, 0, VIS, "extra gap between readout lobes [us]",}

int	ksepi_echogap = 0 with {0, 100ms, 0, VIS, "extra gap between EPI echoes [us]",}

int	ksepi_readsign = 1 with { -1, 1, 1, VIS, "Readout polarity: +1/-1",}

float	ksepi_readampmax = 3.0 with {0.0, 5.0, 3.0, VIS, "Max grad amp for EPI readout lobes",}

float	ksepi_sr = 0.01 with {0.0, , 0.01, VIS, "EPI SR: amp/ramp [(G/cm) / us]",}

int	ksepi_esp = 0 with {0, 1000000, 0, VIS, "View-only: Echo spacing in [us]",}

int	ksepi_blipsign = KS_EPI_POSBLIPS with {KS_EPI_NEGBLIPS, KS_EPI_POSBLIPS, KS_EPI_POSBLIPS, VIS, "Blip polarity: +1/-1",}

int	ksepi_echotime_shifting = 1 with {0, 1, 1, VIS, "Enable echo time shifting for multi shot",}

int	ksepi_kynover = 24 with {KSEPI_MINHNOVER, 512, 24, VIS, "#extralines for MinTE",}

int	ksepi_kznover = 0 with {0, 512, 0, VIS, "#extralines in kz",}

int	ksepi_ky_R = 1 with {1, 512, 1, VIS, "Acceleration in ky",}

int	ksepi_kz_R = 1 with {1, 512, 1, VIS, "Acceleration in kz",}

int	ksepi_kz_nacslines = 16 with {0, 512, 16, VIS, "Number of acs lines in kz",}

int	ksepi_caipi = 0 with {0, 512, 0, VIS, "CAIPIRINHA shift (affects 3D epi only. Set 0 for no CAIPI)",}

int	ksepi_fcy = 1 with {0, 1, 0, VIS, "Flowcomp Y when opfcomp"}

int	ksepi_fcz = 1 with {0, 1, 0, VIS, "Flowcomp Z when opfcomp"}

int	ksepi_fleet = 0 with {0, 1, 0, VIS, "FLEET calibration volume [0:OFF 1:ON]",}

float	ksepi_fleet_flip = 15.0 with {0.1, 90.0, 15.0, VIS, "FLEET flip angle [deg]",}

int	ksepi_fleet_dda = 0 with {0, 200, 0, VIS, "Dummies for FLEET module",}

int	ksepi_fleet_num_ky = 36 with {1, 512, 36, VIS, "Number of ky encodes for FLEET module",}

int	ksepi_fleet_num_kz = 24 with {1, 512, 24, VIS, "Number of kz encodes for FLEET module (3D only)",}

int	ksepi_reflines = 0 with {0, 96, 0, VIS, "Number of phase reference lines per shot",}

int	ksepi_swi_returnmode = 0 with {0, 7, 0, VIS, "SWI recon 0:Off 1:Acq 2:SWI 4:SWIphase",}

int	ksepi_pos_start = KS_RFSSP_PRETIME with {0, , KS_RFSSP_PRETIME, INVIS, "us from start until the first waveform begins",}

int	ksepi_ssi_time = KSEPI_DEFAULT_SSI_TIME with {32, , KSEPI_DEFAULT_SSI_TIME, VIS, "time from eos to ssi in intern trig",}

int	ksepi_dda = 1 with {0, 200, 1, VIS, "Number of dummy scans for steady state",}

int	ksepi_debug = 1 with {0, 100, 1, VIS, "Write out e.g. plot files (unless scan on HW)"}

int	ksepi_imsize = KS_IMSIZE_POW2 with {KS_IMSIZE_NATIVE, KS_IMSIZE_MIN256, KS_IMSIZE_POW2, VIS, "img. upsamp. [0:native 1:pow2 2:min256]"}

int	ksepi_abort_on_kserror = FALSE with {0, 1, 0, VIS, "Hard program abort on ks_error [0:OFF 1:ON]",}

int	ksepi_ghostcorr = 1 with {0, 1, 1, VIS, "Ghost correction [0:OFF 1:ON]",}

int	ksepi_ref_nsegments = 1 with {1, 512, 1, VIS, "Number of kz segments in reference volume",}

int	ksepi_multishot_control = KSEPI_MULTISHOT_B0VOLS with {KSEPI_MULTISHOT_OFF, KSEPI_MULTISHOT_B0VOLS, KSEPI_MULTISHOT_B0VOLS, VIS, "0:PI 1:All MulShot 2:1stMulShot 3:b0MulShot",}

float	ksepi_epiqfact = 1.0 with {1.0, 10.0, 1.0, VIS, "Quetness factor for the EPI readout only",}

KSEPI_SEQUENCE	ksepi = KSEPI_INIT_SEQUENCE

KSEPI_FLEET_SEQUENCE	ksepi_fleetseq = KSEPI_FLEET_INIT_SEQUENCE

int	ksepi_interechotime = 0

float	ksepi_echotime_shifting_shotdelay = 0

int	ksepi_echotime_shifting_sumdelay = 0

int	sequence_iopts []

int	rfspoiling_phase_counter = 0

int	ksepi_diffusion_ramptime = 1500 with {300, 30ms, 1500, VIS, "Ramp times for diffusion gradients", }

float	ksepi_diffusion_maxamp = 0.0 with {0.0, 7.0, 3.0, VIS, "Cap for diffusion gradient amplitude", }

float	ksepi_diffusion_amp = 0.0 with {0.0, 7.0, 0.0, VIS, "View-only: Current diffusion gradient amplitude", }

int	ksepi_diffusion_heat_avg = 1 with {0, 1, 1, VIS, "Root mean sqared averaging diffusion amplitudes heat calculations", }

float	ksepi_diffusion_scaleX_heatcal = 1 with {0, 1, 1, VIS, "View-only: x diffusion gradient amplitude for heating calculations", }

float	ksepi_diffusion_scaleY_heatcal = 1 with {0, 1, 1, VIS, "View-only: y diffusion gradient amplitude for heating calculations", }

float	ksepi_diffusion_scaleZ_heatcal = 1 with {0, 1, 1, VIS, "View-only: z diffusion gradient amplitude for heating calculations", }

int	ksepi_diffusion_echotime = 0 with {0, , 0, VIS, "View-only: Echo time necessary to meet the desired b-value", }

float	ksepi_diffusion_2ndcrushfact = 2.0 with {0.1, 10.0, 2.0, VIS, "Scale factor for 2nd crusher for opdualspinecho",}

int	ksepi_diffusion_returnmode = OFFLINE_DIFFRETURN_ALL with {OFFLINE_DIFFRETURN_ALL, 128, OFFLINE_DIFFRETURN_ALL, VIS, "Diff maps All:0 Acq:1 b0:2 DWI:4 ADC:8 Exp:16 FA:32 cFA:64",}

DIFFSCHEME	diffscheme

int	ndiffdirs = 6

Detailed Description

MR-contrasts supported

Diffusion weighting
T2-w
T2*-w
T2-FLAIR
T2-STIR

Features

ASSET with GE recon
GE-EPI
SE-EPI
T2-FLAIR
DW-EPI (multi-shell (b-value with ALL (3 dirs) and TENSOR)))
Single & dual inversion (FLAIR-block, sliceahead-IR, simple IR) via IR Prep option
Spatial (Graphical) Sat
2D & 3D data acquisition

Macro Definition Documentation

◆ KSEPI_MINHNOVER

#define KSEPI_MINHNOVER 8 /* N.B. overscans below about 16-24 should be avoided for long TE */

◆ KSEPI_MAXRBW_NORAMPSAMPLING

#define KSEPI_MAXRBW_NORAMPSAMPLING 125.0

◆ KSEPI_DEFAULT_SSI_TIME_ICEHARDWARE

#define KSEPI_DEFAULT_SSI_TIME_ICEHARDWARE 100

◆ KSEPI_DEFAULT_SSI_TIME

#define KSEPI_DEFAULT_SSI_TIME 1500

◆ KSEPI_INIT_SEQUENCE1

#define KSEPI_INIT_SEQUENCE1 KS_INIT_SEQ_CONTROL, KS_INIT_EPI, KS_INIT_EPI, KS_INIT_TRAP, KS_INIT_SELRF, KS_INIT_SELRF, KS_INIT_SELRF, KS_INIT_TRAP, KS_INIT_TRAP, KS_INIT_WAIT, KS_INIT_WAIT

◆ KSEPI_INIT_SEQUENCE2

#define KSEPI_INIT_SEQUENCE2 KS_INIT_TRAP, KS_INIT_TRAP, KS_INIT_PHASEENCODING_PLAN, KS_INIT_PHASEENCODING_PLAN, KS_INIT_PHASEENCODING_PLAN, NULL

◆ KSEPI_INIT_SEQUENCE

#define KSEPI_INIT_SEQUENCE {KSEPI_INIT_SEQUENCE1, KSEPI_INIT_SEQUENCE2};

◆ KSEPI_FLEET_INIT_SEQUENCE

#define KSEPI_FLEET_INIT_SEQUENCE {KS_INIT_SEQ_CONTROL, KS_INIT_EPI, KS_INIT_TRAP, KS_INIT_SELRF, KS_INIT_WAIT, KS_INIT_WAIT, KS_INIT_PHASEENCODING_PLAN};

◆ MAX_DIFSCHEME_LENGTH

#define MAX_DIFSCHEME_LENGTH 1024

Typedef Documentation

◆ DIFFSCHEME

typedef float DIFFSCHEME[3][MAX_DIFSCHEME_LENGTH]

Enumeration Type Documentation

◆ KSEPI_MULTISHOT_MODE

enum KSEPI_MULTISHOT_MODE

Enums to switch between multishot vs. parallel imaging modes

Enumerator
KSEPI_MULTISHOT_OFF
KSEPI_MULTISHOT_ALLVOLS
KSEPI_MULTISHOT_1STVOL
KSEPI_MULTISHOT_B0VOLS

              {
   KSEPI_MULTISHOT_OFF, /* 0 */
   KSEPI_MULTISHOT_ALLVOLS, /* 1 */
   KSEPI_MULTISHOT_1STVOL, /* 2 */
   KSEPI_MULTISHOT_B0VOLS, /* 3 */
 } KSEPI_MULTISHOT_MODE;

◆ OFFLINE_DIFFRETURN_MODE

enum OFFLINE_DIFFRETURN_MODE

Enumerator
OFFLINE_DIFFRETURN_ALL
OFFLINE_DIFFRETURN_ACQUIRED
OFFLINE_DIFFRETURN_B0
OFFLINE_DIFFRETURN_MEANDWI
OFFLINE_DIFFRETURN_MEANADC
OFFLINE_DIFFRETURN_EXPATT
OFFLINE_DIFFRETURN_FA
OFFLINE_DIFFRETURN_CFA

              {
   OFFLINE_DIFFRETURN_ALL = 0, 
   OFFLINE_DIFFRETURN_ACQUIRED = 1,
   OFFLINE_DIFFRETURN_B0 = 2,
   OFFLINE_DIFFRETURN_MEANDWI = 4,
   OFFLINE_DIFFRETURN_MEANADC = 8,
   OFFLINE_DIFFRETURN_EXPATT = 16,
   OFFLINE_DIFFRETURN_FA = 32,
   OFFLINE_DIFFRETURN_CFA = 64,
 } OFFLINE_DIFFRETURN_MODE;

Function Documentation

◆ cvinit()

STATUS cvinit ( void )

                     {
   STATUS status;
 
   obl_method = PSD_OBL_OPTIMAL;
 
   status = GEReq_cvinit();
   if (status != SUCCESS) return status;
 
   /* reset debug file ./ks_debug.txt (SIM) or /usr/g/mrraw/ks_debug.txt (HW) */
   ks_dbg_reset();
 
   /* Imaging Options buttons */
   ksepi_init_imagingoptions();
 
   /* Setup UI buttons */
   status = ksepi_init_UI();
   if (status != SUCCESS) return status;
 
   return SUCCESS;
 
 } /* cvinit() */

◆ cveval()

STATUS cveval ( void )

                     {
 
     /*
    cveval() is called 37+ times per UI button push on the MR system, while cvcheck() is only called once.
    For a faster execution we have a my_cveval() function that is called in cvcheck() instead
    */
 
   return SUCCESS;
 }

◆ my_cveval()

STATUS my_cveval ( void )

                        {
   STATUS status;
 
   ks_init_seqcollection(&seqcollection);
 
   status = GEReq_cveval();
   if (status != SUCCESS) return status;
 
   /* User Interface updates & opuserCV sync */
   status = ksepi_eval_UI();
   if (status != SUCCESS) return status;
 
   /* Setup sequence objects */
   status = ksepi_eval_setupobjects();
   if (status != SUCCESS) return status;
 
   /* Calculate minimum (and maximum TE) */
   status = ksepi_eval_TErange();
   if (status != SUCCESS) return status;
 
   /* Run the sequence once (and only once after ksepi_eval_setupobjects()) in cveval() to
      get the sequence duration and the number of object instances (for grad/rf limits in GEReq...limits()) */
   status = ksepi_pg(ksepi_pos_start);
   if (status != SUCCESS) return status;
 
   status = ks_eval_addtoseqcollection(&seqcollection, &ksepi.seqctrl);
   if (status != SUCCESS) return status;
 
   if (ksepi_fleet) {
     status = ksepi_pg_fleet(ksepi_pos_start);
     if (status != SUCCESS) return status;
 
     status = ks_eval_addtoseqcollection(&seqcollection, &ksepi_fleetseq.seqctrl);
     if (status != SUCCESS) return status;
   }
 
   /*--------- Begin: Additional sequence modules -----------*/
 
 
   /* Spatial Sat */
   status = ksspsat_eval(&seqcollection);
   if (status != SUCCESS) return status;
   
   /* ChemSat */
   status = kschemsat_eval(&seqcollection);
   if (status != SUCCESS) return status;
 
   /* Inversion (general & EPI specific). Must be the last sequence module added */
   status = ksepi_eval_inversion(&seqcollection);
   if (status != SUCCESS) return status;
 
 
   /*--------- End: Additional sequence modules -----------*/
 
 
   /* Min TR, #slices per TR, RF/gradient heating & SAR */
   status = ksepi_eval_tr(&seqcollection);
   if (status != SUCCESS) return status;
 
   /* RF scaling across sequence modules */
   status = GEReq_eval_rfscaling(&seqcollection);
   if (status != SUCCESS) return status;
 
   /* scan time */
   status = ksepi_eval_scantime();
   if (status != SUCCESS) return status;
 
   return SUCCESS;
 
 } /* my_cveval() */

◆ cvcheck()

STATUS cvcheck ( void )

                      {
   STATUS status;
 
   status = my_cveval();
   if (status != SUCCESS) return status;
 
   status = GEReq_cvcheck();
   if (status != SUCCESS) return status;
 
   status = ksepi_check();
   if (status != SUCCESS) return status;
 
   abort_on_kserror = ksepi_abort_on_kserror;
 
   return SUCCESS;
 
 } /* cvcheck() */

◆ predownload()

STATUS predownload ( void )

                            {
   STATUS status;
   int numvols2store;
 
   status = GEReq_predownload();
   if (status != SUCCESS) return status;
 
   /* Set filter slot # for SCAN, APS2, MPS2 */
   GEReq_predownload_setfilter(&ksepi.epitrain.read.acq.filt);
   ksepi.dynreftrain.read.acq.filt.fslot = ksepi.epitrain.read.acq.filt.fslot;
   ksepi_fleetseq.epitrain.read.acq.filt.fslot = ksepi.epitrain.read.acq.filt.fslot;
 
   /* slice ordering */
   /* The following GE globals must be set appropriately:
      data_acq_order[], rsp_info[], rsprot[], rsptrigger[]. This is a must for a main pulse sequence */
   if (opimode == PSD_2D) {
     status = GEReq_predownload_store_sliceplan(ks_slice_plan);
   } else {
     status = GEReq_predownload_store_sliceplan3D(opslquant, opvquant);
   }
   if (status != SUCCESS) return status;
 
   /* generic rh-vars setup */
   numvols2store = ksepi_fleet + ksepi_ghostcorr + opfphases;
   rhnecho = opnecho + (ksepi_reflines > 0);
   status = GEReq_predownload_setrecon_epi(&ksepi.epitrain, numvols2store, ks_slice_plan, ksepi_interechotime - ksepi.epitrain.duration, ksepi_blipsign, 0, ksepi_multishot_control > 0, ksepi_ghostcorr, ksepi_imsize);
   if (status != SUCCESS) return status;
 
   /* KSInversion predownload */
   status = ksinv_predownload_setrecon();
   if (status != SUCCESS) return status;
 
   /* Diffusion predownload */
   status = ksepi_diffusion_predownload_setrecon();
   if (status != SUCCESS) return status;
 
   /* further sequence specific recon settings that have not been set correctly at this point */
   status = ksepi_predownload_setrecon();
   if (status != SUCCESS) return status;
 
   /* plotting of sequence modules and slice timing to disk */
   ksepi_predownload_plot(&seqcollection);
 
   return SUCCESS;
 
 } /* predownload() */

◆ pulsegen()

STATUS pulsegen ( void )

                         {
 
   GEReq_pulsegenBegin();
 
   /* Main Pulse Sequence */
   ksepi_pg(ksepi_pos_start);
   KS_SEQLENGTH(seqcore, ksepi.seqctrl);
 
   /* Spatial Sat */
   ksspsat_pulsegen();
 
   /* ChemSat sequence module */
   kschemsat_pg(&kschemsat);
   KS_SEQLENGTH(seqKSChemSat, kschemsat.seqctrl); /* does nothing if kschemsat.seqctrl.duration = 0 */
 
   /* Inversion sequence modules */
   ksinv_pulsegen();
 
   /* FLEET module */
   ksepi_pg_fleet(ksepi_pos_start);
   KS_SEQLENGTH(seqFLEET, ksepi_fleetseq.seqctrl);
 
   GEReq_pulsegenEnd();
 
   buildinstr(); /* load the sequencer memory */
 
 
   return SUCCESS;
 
 } /* pulsegen() */

◆ mps2()

STATUS mps2 ( void )

                   {
 
   rspent = L_MPS2;
   strcpy(psdexitarg.text_arg, "mps2");
 
   if (ksepi_scan_init() == FAILURE)
     return rspexit();
 
   if (ksepi_scan_prescanloop(30000, ksepi_dda) == FAILURE)
     return rspexit();
 
   rspexit();
 
  return SUCCESS;
 
 } /* mps2() */

◆ aps2()

STATUS aps2 ( void )

                   {
 
   rspent = L_APS2;
   strcpy(psdexitarg.text_arg, "aps2");
 
   if (ksepi_scan_init() == FAILURE)
     return rspexit();
 
   if (ksepi_scan_prescanloop(100, ksepi_dda) == FAILURE)
     return rspexit();
 
   rspexit();
 
   return SUCCESS;
 
 } /* aps2() */

◆ scan()

STATUS scan ( void )

                   {
 
   rspent = L_SCAN;
   strcpy(psdexitarg.text_arg, "scan");
 
   if (ksepi_scan_init() == FAILURE)
     return rspexit();
 
   /* Scan hierarchy:
 
     Without inversion:
     ksepi_scan_scanloop() - Data for the entire scan
         ksepi_scan_acqloop() - All data for one set of slices that fit within one TR (one acquisition)
             ksepi_scan_sliceloop() - One set of slices that fit within one TR played out for one shot
                  ksepi_scan_coreslice() - One slice playout, with optional other sequence modules
 
     With inversion:
     ksepi_scan_scanloop() - Data for the entire scan
         ksepi_scan_acqloop() - All data for one set of slices that fit within one TR (one acquisition)
             ksinv_scan_sliceloop() - One set of slices that fit within one TR played out for one shot
                                      using the sliceloop in KSInversion.e. Note that ksinv_scan_sliceloop()
                                      takes over the TR timing from ksepi_scan_sliceloop() and uses a
                                      function pointer to ksepi_scan_coreslice_nargs() to execute the
                                      contents of ksepi_scan_coreslice().
   */
   ksepi_scan_scanloop();
 
   GEReq_endofpassandscan();
 
   /* So we can see the sequence in plotter after scan completes */
   ks_scan_switch_to_sequence(&ksepi.seqctrl);
 
   rspexit();
 
   return SUCCESS;
 
 }   /* scan() */

◆ abstract()

abstract ( "EPI " [KSFoundation] )

◆ psdname()

psdname ( "ksepi" )

◆ ksepi_eval_flowcomp_phase()

STATUS ksepi_eval_flowcomp_phase	(	KS_TRAP *	fcphase,
		const KS_EPI *	epi,
		const char *	desc
	)

                                                                                         {
 
   /* set time origin at end of bipolar flow comp lobe/beginning of epi.blipphaser */
   float dummy1 = 0.0;
   float dummy2 = 0.0;
   float zeromomentsum = 0.0;
   float firstmomentsum = 0.0;
   int pulsepos = 0;
   int invertphase = 0;
   int pulsecnt;
   int epiesp = 0;
   
   epiesp = (epi->read.grad.duration + epi->read_spacing);
 
   /* compute moments for blips */
   pulsepos = epi->blipphaser.grad.duration + epiesp - epi->blip.duration / 2;
   
   int blips2cent = ((epi->blipphaser.nover != 0) ? (epi->blipphaser.nover / epi->blipphaser.R) : (epi->etl / 2)) - 1;
 
   for (pulsecnt = 0; pulsecnt < blips2cent; pulsecnt++) {
     /* N.B.: pulsepos is updated in rampmoments() */
     rampmoments(0.0,           epi->blip.amp, epi->blip.ramptime,    invertphase, &pulsepos, &dummy1, &dummy2, &zeromomentsum, &firstmomentsum);
     rampmoments(epi->blip.amp, epi->blip.amp, epi->blip.plateautime, invertphase, &pulsepos, &dummy1, &dummy2, &zeromomentsum, &firstmomentsum);
     rampmoments(epi->blip.amp, 0.0,           epi->blip.ramptime,    invertphase, &pulsepos, &dummy1, &dummy2, &zeromomentsum, &firstmomentsum);
     pulsepos += (epiesp - epi->blip.duration);
   }
 
   ks_init_trap(fcphase);
 
   if (!areSame(zeromomentsum, 0) && !areSame(firstmomentsum, 0)) {
     int fcramp, fcplateau, dummy;
     float fcamp;
     amppwygmn(zeromomentsum, firstmomentsum, epi->blipphaser.grad.ramptime, epi->blipphaser.grad.plateautime, epi->blipphaser.grad.ramptime, 
               0.0, 0.0, (double) ks_syslimits_ampmax(loggrd), (double) ks_syslimits_ramptimemax(loggrd), 0, 
               &fcramp, &fcplateau, &dummy, &fcamp);
 
     fcphase->amp = fcamp;
     fcphase->ramptime = fcramp;
     fcphase->plateautime = fcplateau;
     fcphase->duration = 2 * fcphase->ramptime + fcphase->plateautime;
     fcphase->area = fcphase->duration * ((float) fcphase->ramptime + fcphase->plateautime);
     sprintf(fcphase->description, desc);
   }
 
   return SUCCESS;
 
 } /* ksepi_eval_flowcomp() */

◆ ksepi_pg()

STATUS ksepi_pg ( int start_time )

The ksepi (main) pulse sequence

This is the main pulse sequence in ksepi.e using the sequence objects in KSEPI_SEQUENCE with the sequence module name "ksepimain" (= ksepi.seqctrl.description)

Return values

STATUS SUCCESS or FAILURE

                                 {
   KS_SEQLOC tmploc = KS_INIT_SEQLOC;
   int epi_startpos = KS_NOTSET;
   int epi_readout_startpos = KS_NOTSET;
   int fc_startpos = KS_NOTSET;
   int fcz_endpos = KS_NOTSET;
   int echo, board;
 
   if (start_time < KS_RFSSP_PRETIME) {
     return ks_error("%s: 1st arg (pos start) must be at least %d us", __FUNCTION__, KS_RFSSP_PRETIME);
   }
 
 #ifdef HOST_TGT
   if (opte < avminte) {
     /* we cannot proceed until TE is in range.
        Return a long seq duration and pretend all is good */
     ks_eval_seqctrl_setminduration(&ksepi.seqctrl, 1s);
     return SUCCESS;
   }
 #endif
 
 
   /*******************************************************************************************************
    *  RF Excitation
    *******************************************************************************************************/
   tmploc.ampscale = 1.0;
   tmploc.pos = RUP_GRD(start_time + KS_RFSSP_PRETIME);
   tmploc.board = ZGRAD;
 
   /* N.B.: ks_pg_selrf()->ks_pg_rf() detects that ksepi.selrfexc is an excitation pulse
      (ksepi.selrfexc.rf.role = KS_RF_ROLE_EXC) and will also set ksepi.seqctrl.momentstart
      to the absolute position in [us] of the isocenter of the RF excitation pulse */
   if (ks_pg_selrf(&ksepi.selrfexc, tmploc, &ksepi.seqctrl) == FAILURE)
     return FAILURE;
 
   /* forward to end of selrfexc.postgrad (works for when slice sel gradient is KS_TRAP or KS_WAVE as only
      one of them can have non-zero duration at a given time) */
   tmploc.pos += ksepi.selrfexc.pregrad.duration + ksepi.selrfexc.grad.duration + ksepi.selrfexc.gradwave.duration + ksepi.selrfexc.postgrad.duration;
   
   /*******************************************************************************************************
   *  Flow clomp in slice dir
   *******************************************************************************************************/
 
   /* First flow comp gradient was already merged into selrf rephaser */
   /* Second flow comp gradient slice for slice excitation */
   if (ks_pg_trap(&ksepi.fcompslice, tmploc, &ksepi.seqctrl) == FAILURE) /* N.B.: will return quietly if ksepi.fcompslice.duration = 0 (opfcomp = 0) */
     return FAILURE;
   fcz_endpos = tmploc.pos + ksepi.fcompslice.duration;
 
   /*******************************************************************************************************
   *  EPI phase reference lines
   *******************************************************************************************************/
   tmploc.board = (ksepi_slicecheck) ? KS_FREQZ_PHASEY : KS_FREQX_PHASEY;
   tmploc.pos = fcz_endpos;
   if (ksepi_slicecheck == FALSE) { /* reflines dephaser may overlap with slice flow comp and selrf rephaser unless slicecheck mode */
     tmploc.pos -= IMin(2, ksepi.dynreftrain.readphaser.duration, ksepi.selrfexc.postgrad.duration + ksepi.fcompslice.duration);
   }
   tmploc.ampscale = ksepi_readsign;
   if (ks_pg_epi(&ksepi.dynreftrain, tmploc, &ksepi.seqctrl) == FAILURE)
     return FAILURE;
 
   /*******************************************************************************************************
   *  EPI trains: Begin   (> 1 only supported with offline recon)
   -------------------------------------------------------------------------------------------------------*/
   for (echo = 0; echo < opnecho; echo++) {
 
     if (acq_type == TYPSPIN) {
       if (opdiffuse && echo == 0) {
         if (ksepi_diffusion_pg(&ksepi, opte) == FAILURE)
           return FAILURE;
       } else {
         if (echo == 0) /* RF refocusing pulse for 1st EPI train at TE/2 */
           tmploc.pos = ksepi.seqctrl.momentstart + opte / 2 - ksepi.selrfref.rf.start2iso - ksepi.selrfref.grad.ramptime - ksepi.selrfref.pregrad.duration;
         else /* RF refocusing pulse between two EPI trains (2nd-Nth EPI train are played out as tight as possible when ksepi_echogap = 0). Use epi_startpos from previous echo index (see below) */
           tmploc.pos = epi_startpos + ksepi.epitrain.duration + KS_RFSSP_PRETIME + ksepi_echogap / 2;
         tmploc.board = ZGRAD;
         if (ks_pg_selrf(&ksepi.selrfref, tmploc, &ksepi.seqctrl) == FAILURE)
           return FAILURE;
       }
     } /* acq_type == TYPSPIN */
 
     epi_startpos = ksepi.seqctrl.momentstart + opte - ksepi.epitrain.time2center + (echo * ksepi_interechotime);
     epi_readout_startpos = epi_startpos + IMax(3, ksepi.epitrain.readphaser.duration,
                                                   ksepi.epitrain.blipphaser.grad.duration,
                                                   ksepi.epitrain.zphaser.grad.duration);
 
     /*******************************************************************************************************
     *  Flow comp in phase dir
     *******************************************************************************************************/
     
     fc_startpos = epi_readout_startpos - ksepi.epitrain.blipphaser.grad.duration - 2 * ksepi.fcompphase.duration;
     tmploc.board = YGRAD;
     tmploc.pos = fc_startpos;
     tmploc.ampscale = 1;
     if (ks_pg_trap(&ksepi.fcompphase, tmploc, &ksepi.seqctrl) == FAILURE) /* instance #0. N.B.: will return quietly if ksepi.fcompphase.duration = 0 */
       return FAILURE;
 
     tmploc.pos += ksepi.fcompphase.duration;
     tmploc.ampscale = -1;
     if (ks_pg_trap(&ksepi.fcompphase, tmploc, &ksepi.seqctrl) == FAILURE) /* instance #1 */
       return FAILURE;
 
     /*******************************************************************************************************
     *  EPI readout including de/rephasers on freq, phase and slice encoding axes (net zero moment on both axes)
     *******************************************************************************************************/
     
     tmploc.board = (ksepi_slicecheck) ? KS_FREQZ_PHASEY : KS_FREQX_PHASEY;
     tmploc.pos = epi_startpos;
     tmploc.ampscale = ksepi_readsign;
     if (ks_pg_epi(&ksepi.epitrain, tmploc, &ksepi.seqctrl) == FAILURE)
       return FAILURE;
 
     /*******************************************************************************************************
     *  EPI echo time shifting
     *******************************************************************************************************/
     if (ksepi_echotime_shifting == TRUE && echo == 0) {
       for (board = XGRAD; board <= SSP; board++) {
         tmploc.board = board;
         if (oppseq == PSD_SE) {
           /* 2D: SE-EPI or DW-EPI */
           tmploc.pos = epi_startpos - GRAD_UPDATE_TIME;
         } else {
           /* 2D/3D: GE-EPI
           Place wait pulses just before main epi train dephasers (incl flowcomp if present) */
             if ((board == XGRAD && ksepi_slicecheck == FALSE) || (board == ZGRAD && ksepi_slicecheck == TRUE)) {
             tmploc.pos = epi_readout_startpos - ksepi.epitrain.readphaser.duration - GRAD_UPDATE_TIME;
           } else if (board == YGRAD) {
             tmploc.pos = fc_startpos - GRAD_UPDATE_TIME;
           } else {
             tmploc.pos = epi_readout_startpos - ksepi.epitrain.zphaser.grad.duration - GRAD_UPDATE_TIME;
           }
         }
         if (ks_pg_wait(&ksepi.pre_delay, tmploc, &ksepi.seqctrl) != SUCCESS) {
           return FAILURE;
         }
       }
     }
 
 
   }
   /*------------------------------------------------------------------------------------------------------
    *  EPI trains: End
    *******************************************************************************************************/
 
   /*******************************************************************************************************
    *  Gradient spoilers on Y and Z (at the same time)
    *******************************************************************************************************/
   tmploc.ampscale = 1.0;
   tmploc.pos = epi_startpos + ksepi.epitrain.duration;
   tmploc.board = YGRAD;
   if (ks_pg_trap(&ksepi.spoiler, tmploc, &ksepi.seqctrl) == FAILURE)
     return FAILURE;
   tmploc.board = ZGRAD;
   if (ks_pg_trap(&ksepi.spoiler, tmploc, &ksepi.seqctrl) == FAILURE)
     return FAILURE;
 
   tmploc.pos += ksepi.spoiler.duration;
 
   /*******************************************************************************************************
   *  EPI echo time shifting (post EPI readouts)
   *******************************************************************************************************/
   if (ksepi_echotime_shifting == TRUE) {
     tmploc.pos += GRAD_UPDATE_TIME;
     tmploc.board = KS_ALL;
     if (ks_pg_wait(&ksepi.post_delay, tmploc, &ksepi.seqctrl) != SUCCESS) {
       return FAILURE;
     }
     tmploc.pos += IMax(2, psd_grd_wait, psd_rf_wait) + GRAD_UPDATE_TIME;
     tmploc.pos += ksepi_echotime_shifting_sumdelay;
   }
 
   /*******************************************************************************************************
    *  Set the minimal sequence duration (ksepi.seqctrl.min_duration) by calling
    *  ks_eval_seqctrl_setminduration()
    *******************************************************************************************************/
 
   /* make sure we are divisible by GRAD_UPDATE_TIME (4us) */
   tmploc.pos = RUP_GRD(tmploc.pos);
 
 #ifdef HOST_TGT
   /* On HOST only: Sequence duration (ksepi.seqctrl.ssi_time must be > 0 and is added to ksepi.seqctrl.min_duration in ks_eval_seqctrl_setminduration() */
   ksepi.seqctrl.ssi_time = ksepi_eval_ssitime();
   ks_eval_seqctrl_setminduration(&ksepi.seqctrl, tmploc.pos); /* tmploc.pos now corresponds to the end of last gradient in the sequence */
 #endif
 
   /*******************************************************************************************************
    * Phase encoding table
    *
    * Need to call this in ksepi_pg() so it is run both on HOST and TGT. This, since the phase table
    * is dynamically allocated in ks_phaseencoding_generate_epi()->ks_phaseencoding_resize()
    *******************************************************************************************************/
   if (ks_phaseencoding_generate_epi(&ksepi.full_peplan, "Fully sampled EPI volume",
                                       &ksepi.epitrain, 
                                       (ks_enum_epiblipsign) ksepi_blipsign,
                                       KS_PF_EARLY_TE,
                                       ksepi.epitrain.blipphaser.R, 
                                       (ks_enum_sweep_order) KS_SWEEP_ORDER_TOP_DOWN,
                                       ksepi.epitrain.zphaser.numlinestoacq, 
                                       ksepi_caipi) == FAILURE) {
     return FAILURE;
   }
   if (ks_phaseencoding_generate_epi(&ksepi.ref_peplan, "EPI reference volume",
                                       &ksepi.epitrain, 
                                       (ks_enum_epiblipsign) ksepi_blipsign,
                                       KS_PF_EARLY_TE,
                                       ksepi.epitrain.blipphaser.R,
                                       (ks_enum_sweep_order) KS_SWEEP_ORDER_TOP_DOWN,
                                       ksepi_ref_nsegments,
                                       ksepi_caipi) == FAILURE) {
     return FAILURE;
   }
   if (ks_phaseencoding_generate_epi(&ksepi.peplan, "Accelerated EPI volume",
                                       &ksepi.epitrain,
                                       (ks_enum_epiblipsign) ksepi_blipsign,
                                       KS_PF_EARLY_TE,
                                       ksepi.epitrain.blipphaser.R / ksepi_ky_R,
                                       (ks_enum_sweep_order) KS_SWEEP_ORDER_TOP_DOWN,
                                       ksepi.epitrain.zphaser.numlinestoacq,
                                       ksepi_caipi) == FAILURE) {
     return FAILURE;
   }
   ksepi.current_peplan = &ksepi.full_peplan;
 
   /* KS_NOTSET -> turns off phase blips for phase reference lines */
   ks_scan_epi_shotcontrol(&ksepi.dynreftrain, 0, ks_scan_info[0], NULL, 0, /* exc */ KS_NOTSET, 0);
 
   /* set EPI dephasers and blips to the first shot so we get the correct plots in WTools */
   ks_scan_epi_shotcontrol(&ksepi.epitrain, 0, ks_scan_info[0], &ksepi.full_peplan, 0, /* exc */ 0, 0);
 
   return SUCCESS;
 
 } /* ksepi_pg() */

◆ ksepi_scan_coreslice()

int ksepi_scan_coreslice	(	const SCAN_INFO *	slice_pos,
		int	dabslice,
		int	shot
	)

Plays out one slice in real time during scanning together with other active sequence modules

On TGT on the MR system (PSD_HW), this function sets up (ksepi_scan_seqstate()) and plays out the core ksepi sequence with optional sequence modules also called in this function. The low-level function call startseq(), which actually starts the realtime sequence playout is called from within ks_scan_playsequence(), which in addition also returns the time to play out that sequence module (see time += ...).

On HOST (in ksepi_eval_tr()) we call ksepi_scan_sliceloop_nargs(), which in turn calls this function that returns the total time in [us] taken to play out this core slice. These times are increasing in each parent function until ultimately ksepi_scan_scantime(), which returns the total time of the entire scan.

After each call to ks_scan_playsequence(), ks_plot_slicetime() is called to add slice-timing information on file for later PDF-generation of the sequence. As scanning is performed in real-time and may fail if interrupted, ks_plot_slicetime() will return quietly if it detects both IPG (TGT) and PSD_HW (on the MR scanner). See predownload() for the PNG/PDF generation.

Parameters

[in]	slice_pos	Position of the slice to be played out (one element in the global `ks_scan_info[]` array)
[in]	dabslice	0-based slice index for data storage
[in]	shot	Linear ky kz `shot` index in range `[0, (ksepi.peplan.num_shots-1)]`

Return values

coreslicetime Time taken in [us] to play out one slice with potentially other sequence modules

                                                                                {
   int echo;
   int time = 0;
   float tloc = 0.0;
   SCAN_INFO slice_pos_updated;
   KS_MAT4x4 Mphysical = KS_MAT4x4_IDENTITY;
   const KS_MAT4x4 Identity = KS_MAT4x4_IDENTITY;
 
   if (slice_pos != NULL)
     tloc = slice_pos->optloc;
 
   /*******************************************************************************************************
   * Update slice info
   *******************************************************************************************************/
   if (slice_pos != NULL) {
     ks_scan_update_slice_location(&slice_pos_updated, *slice_pos, Mphysical, Identity);
   }
 
   /*******************************************************************************************************
   * SpSat sequence module
   *******************************************************************************************************/
   time += ksspsat_scan_playsequences(ks_perform_slicetimeplot);
 
 
   /*******************************************************************************************************
   * Chemsat sequence module
   *******************************************************************************************************/
   kschemsat_scan_seqstate(&kschemsat);
   time += ks_scan_playsequence(&kschemsat.seqctrl);
   ks_plot_slicetime(&kschemsat.seqctrl, 1, NULL, KS_NOTSET, slice_pos == NULL ? KS_PLOT_NO_EXCITATION : KS_PLOT_STANDARD); /* no slice location for fat sat */
 
 
   /*******************************************************************************************************
   * ksepi main sequence module
   *******************************************************************************************************/
   if (slice_pos != NULL) {
     /* modify sequence for next playout. If not entry point scan (e.g. L_REF), use no ky phase encodes */
     ksepi_scan_seqstate(slice_pos_updated, (rspent == L_SCAN) ? shot : KS_NOTSET);
   } else {
     /* false slice, shut off RF */
     ksepi_scan_rf_off();
   }
 
   /* data routing control */
   KS_PHASEENCODING_COORD coord = ks_phaseencoding_get(ksepi.current_peplan, 0, shot); /* coord to first line of EPI train */
   if (KS_3D_SELECTED) {
     if (ks_scan_info[1].optloc > ks_scan_info[0].optloc)
       dabslice = (opslquant * opvquant - 1) - coord.kz;
     else
       dabslice = coord.kz;
   }
   for (echo = 0; echo < opnecho; echo++) {
     ks_scan_epi_loadecho(&ksepi.epitrain, echo, echo, dabslice, ksepi.current_peplan, shot);
   }
   if (ksepi_reflines > 0) {
     /* store phase reference lines as opnecho:th echo */
     ks_scan_epi_loadecho(&ksepi.dynreftrain, 0, opnecho, dabslice, ksepi.current_peplan, shot);
   }
 
   time += ks_scan_playsequence(&ksepi.seqctrl);
   ks_plot_slicetime(&ksepi.seqctrl, 1, &tloc, opslthick, slice_pos == NULL ? KS_PLOT_NO_EXCITATION : KS_PLOT_STANDARD);
 
   return time; /* in [us] */
 
 } /* ksepi_scan_coreslice() */

◆ ksepi_scan_coreslice_nargs()

int ksepi_scan_coreslice_nargs	(	const SCAN_INFO *	slice_pos,
		int	dabslice,
		int	nargs,
		void **	args
	)

Wrapper function to ksepi_scan_coreslice() with standardized input arguments

KSInversion.e has functions (ksinv_eval_multislice(), ksinv_eval_checkTR_SAR() and ksinv_scan_sliceloop()) that expect a standardized function pointer to the coreslice function of a main sequence. When inversion mode is enabled for the sequence, ksinv_scan_sliceloop() is used instead of ksepi_scan_sliceloop() in ksepi_scan_acqloop(), and the generic ksinv_scan_sliceloop() function need a handle to the coreslice function of the main sequence.

In order for these ksinv_*** functions to work for any pulse sequence they need a standardized function pointer with a fixed set of input arguments. As different pulse sequences may need different number of input arguments (with different meaning) this ksepi_scan_coreslice_nargs() wrapper function provides the argument translation for ksepi_scan_coreslice().

The function pointer must have SCAN_INFO and slice storage index (dabslice) as the first two input args, while remaining input arguments (to ksepi_scan_coreslice()) are stored in the generic void pointer array with nargs elements, which is then unpacked before calling ksepi_scan_coreslice().

Parameters

[in]	slice_pos	Pointer to the SCAN_INFO struct corresponding to the current slice to be played out
[in]	dabslice	0-based slice index for data storage
[in]	nargs	Number of extra input arguments to ksepi_scan_coreslice() in range [0,2]
[in]	args	Void pointer array pointing to the variables containing the actual values needed for ksepi_scan_coreslice()

Return values

coreslicetime Time taken in [us] to play out one slice with potentially other sequence modules

                                                                                                  {
   int shot = 0;
 
   if (nargs < 0 || nargs > 1) {
     ks_error("%s: 4th arg (void **) must contain 0-1 elements (shot), not %d", __FUNCTION__, nargs);
     return -1;
   } else if (nargs > 0 && args == NULL) {
     ks_error("%s: 4th arg (void **) cannot be NULL if nargs (3rd arg) != 0", __FUNCTION__);
     return -1;
   }
 
   if (nargs >= 1 && args[0] != NULL) {
     shot = *((int *) args[0]);
   }
 
   return ksepi_scan_coreslice(slice_pos, dabslice, shot); /* in [us] */
 
 } /* ksepi_scan_coreslice_args() */

◆ ksepi_scan_sliceloop()

int ksepi_scan_sliceloop	(	int	slperpass,
		int	volindx,
		int	passindx,
		int	shot
	)

Plays out `slperpass` slices corresponding to one TR

This function gets a spatial slice location index based on the pass index and temporal position within current pass. It then calls ksepi_scan_coreslice() to play out one coreslice (i.e. the main ksepi main sequence + optional sequence modules, excluding inversion modules).

Parameters

[in]	slperpass	Number of slices to play in the slice loop
[in]	volindx	Volume index in range `[0, opfphases - 1]`
[in]	passindx	Pass index in range `[0, ks_slice_plan.npasses - 1]`
[in]	shot	Linear ky kz `shot` index in range `[0, (ksepi.peplan.num_shots-1)]`

Return values

slicelooptime Time taken in [us] to play out slperpass slices

                                                                              {
   int time = 0;
   int slloc, sltimeinpass;
   SCAN_INFO centerposition = ks_scan_info[0]; /* first slice chosen here, need only rotation stuff */
 
   (void) volindx;
 
   if (KS_3D_SELECTED) {
     int centerslice = opslquant/2;
     /* for future 3D multislab support, let passindx update centerposition */
     centerposition.optloc = (ks_scan_info[centerslice-1].optloc + ks_scan_info[centerslice].optloc)/2.0;
   }
 
 
   for (sltimeinpass = 0; sltimeinpass < slperpass; sltimeinpass++) {
 
     SCAN_INFO *current_slice = &centerposition;
     if (!KS_3D_SELECTED) {
       /* slice location from slice plan */
       slloc = ks_scan_getsliceloc(&ks_slice_plan, passindx, sltimeinpass);
       current_slice = (slloc != KS_NOTSET) ? &ks_scan_info[slloc] : NULL;
     }
     time += ksepi_scan_coreslice(current_slice, sltimeinpass, shot);
 
   }
 
   return time; /* in [us] */
 
 } /* ksepi_scan_sliceloop() */

◆ ksepi_scan_sliceloop_nargs()

int ksepi_scan_sliceloop_nargs	(	int	slperpass,
		int	nargs,
		void **	args
	)

Wrapper function to ksepi_scan_sliceloop() with standardized input arguments

For TR timing heat/SAR calculations of regular 2D multislice sequences, GEReq_eval_TR(), ks_eval_mintr() and GEReq_eval_checkTR_SAR() use a standardized function pointer with a fixed set of input arguments to call the sliceloop of the main sequence with different number of slices to check current slice loop duration. As different pulse sequences may need different number of input arguments (with different meaning) this ksepi_scan_sliceloop_nargs() wrapper function provides the argument translation for ksepi_scan_sliceloop().

The function pointer must have an integer corresponding to the number of slices to use as its first argument while the remaining input arguments (to ksepi_scan_sliceloop()) are stored in the generic void pointer array with nargs elements, which is then unpacked before calling ksepi_scan_sliceloop().

Parameters

[in]	slperpass	Number of slices to play in the slice loop
[in]	nargs	Number of extra input arguments to ksepi_scan_sliceloop() in range [0,3]
[in]	args	Void pointer array pointing to the variables containing the actual values needed for ksepi_scan_sliceloop()

Return values

slicelooptime Time taken in [us] to play out slperpass slices

                                                                       {
   int volindx = 0;
   int passindx = 0;
   int shot = KS_NOTSET; /* off */
 
   if (nargs < 0 || nargs > 3) {
     ks_error("%s: 3rd arg (void **) must contain up to 3 elements: volindx, passindx, shot. Not %d", __FUNCTION__, nargs);
     return -1;
   } else if (nargs > 0 && args == NULL) {
     ks_error("%s: 3rd arg (void **) cannot be NULL if nargs (2nd arg) != 0", __FUNCTION__);
     return -1;
   }
 
   if (nargs >= 1 && args[0] != NULL) {
     volindx = *((int *) args[0]);
   }
   if (nargs >= 2 && args[1] != NULL) {
     passindx = *((int *) args[1]);
   }
   if (nargs >= 3 && args[2] != NULL) {
     shot = *((int *) args[2]);
   }
 
   return ksepi_scan_sliceloop(slperpass, volindx, passindx, shot); /* in [us] */
 
 } /* ksepi_scan_sliceloop_nargs() */

◆ ksepi_scan_seqstate()

STATUS ksepi_scan_seqstate	(	SCAN_INFO	slice_info,
		int	shot
	)

Sets the current state of all ksepi sequence objects being part of KSEPI_SEQUENCE

This function sets the current state of all ksepi sequence objects being part of KSEPI_SEQUENCE, incl. gradient amplitude changes, RF freq/phases and receive freq/phase based on current slice position and phase encoding indices.

The idea of having a 'seqstate' function is to be able to come back to a certain sequence state at any time and possibly play it out once more. This could for example be useful when certain lines or slices need to be rescanned due to image artifacts detected during scanning.

Parameters

[in]	slice_info	Position of the slice to be played out (one element in the `ks_scan_info[]` array)
[in]	shot	Linear ky kz `shot` index in range `[0, (ksepi.peplan.num_shots-1)]`

Return values

STATUS SUCCESS or FAILURE

                                                            {
   int echo;
   float exc_rfphase;
   int exc = 0; /* NEX index. Future use */
 
   /* RF frequency & phase */
   if (ksepi_rfspoiling) {
     exc_rfphase = ks_scan_rf_phase_spoiling(rfspoiling_phase_counter);
     rfspoiling_phase_counter++;
   } else {
     exc_rfphase = 0;
   }
 
 
   ks_scan_rotate(slice_info);
 
   ks_scan_rf_on(&ksepi.selrfexc.rf, INSTRALL);
   ks_scan_rf_on(&ksepi.selrfref.rf, INSTRALL);
 
   ks_scan_selrf_setfreqphase(&ksepi.selrfexc, 0,        slice_info, exc_rfphase);
   ks_scan_selrf_setfreqphase(&ksepi.selrfref, INSTRALL, slice_info, exc_rfphase+90);
 
   if (opdiffuse && opdualspinecho) {
     ks_scan_rf_on(&ksepi.selrfref2.rf, 0);
     ks_scan_selrf_setfreqphase(&ksepi.selrfref2, 0, slice_info, exc_rfphase+90);
   }
 
   /* EPI echoes (i.e. EPI trains) */
   for (echo = 0; echo < opnecho; echo++) {
     ks_scan_epi_shotcontrol(&ksepi.epitrain, echo, slice_info, ksepi.current_peplan, shot, exc, exc_rfphase);
   } /* opnecho */
   ks_scan_epi_shotcontrol(&ksepi.dynreftrain, 0, slice_info, NULL, KS_NOTSET, KS_NOTSET, exc_rfphase);
 
   return SUCCESS;
 
 } /* ksepi_scan_seqstate() */

◆ ksepi_scan_acqloop()

float ksepi_scan_acqloop	(	int	passindx,
		int	volindx,
		int	multishotflag
	)

Plays out all phase encodes for all slices belonging to one pass

This function traverses through all shots (ksepi_numshots) to be played out and runs the ksepi_scan_sliceloop() for each set of shots and excitation. If ksepi_dda > 0, dummy scans will be played out before the phase encoding begins.

In the case of inversion, ksinv_scan_sliceloop() is called instead of ksepi_scan_sliceloop(), where the former takes a function pointer to ksepi_scan_coreslice_nargs() in order to be able to play out the coreslice in a timing scheme set by ksinv_scan_sliceloop().

Parameters

[in]	passindx	0-based pass index in range `[0, ks_slice_plan.npasses - 1]`
[in]	volindx	0-based image volume index in range `[0, opfphases - 1]`
[in]	multishotflag	ksepi.epitrain.blipphaser.R is used as... 0: Parallel imaging factor 1: Multi-shot (all volumes, KSEPI_MULTISHOT_ON) 2: Multi-shot (multishot vol 1 (volindx=0), PI for vols 2-N, KSEPI_MULTISHOT_ON_VOL1) 3: Multi-shot (multishot for b0 volumes), PI for diffusion volumes (only when opdiffuse > 0)

Return values

passlooptime Time taken in [us] to play out all phase encodes and excitations for slperpass slices. Note that the value is a float instead of int to avoid int overrange at 38 mins of scanning

                                                                        {
   float time = 0.0;
   int shot, kyshot;
   KS_PHASEENCODING_COORD coord;
   int ndummies = 0;
   int is_multishot = (multishotflag == KSEPI_MULTISHOT_ALLVOLS) || \
                      (multishotflag == KSEPI_MULTISHOT_1STVOL && (volindx == 0)) || \
                      (multishotflag == KSEPI_MULTISHOT_B0VOLS && opdiffuse && (volindx < opdifnumt2));
 
   if (ksepi_ghostcorr && volindx == -1) { /* reference volume */
     ksepi.current_peplan = &ksepi.ref_peplan;
   } else if (is_multishot) { /* multishot volume */
     ksepi.current_peplan = &ksepi.full_peplan;
   } else { /* accelerated volume */
     ksepi.current_peplan = &ksepi.peplan;
   }
 
   if (ksepi_fleet && volindx == -ksepi_fleet - ksepi_ghostcorr) { /* FLEET volume */
     time += (float) ksepi_fleet_scan_sliceloop(ks_slice_plan.nslices_per_pass, volindx, passindx);
   }
   else { /* non-FLEET volumes */
     if (volindx == 0)
       ndummies = ksepi_dda;
     else
       ndummies = 0;
 
     for (shot = -ndummies; shot < ksepi.current_peplan->num_shots; shot++) {
 
       if (shot == 0 && ndummies > 0) {
         ks_plot_slicetime_endofpass(KS_PLOT_PASS_WAS_DUMMY);
       }
 
       if (ksepi_echotime_shifting == TRUE) {
         coord = ks_phaseencoding_get(ksepi.current_peplan, 0, shot); /* coord to first line of EPI train */
         kyshot = coord.ky % ksepi.current_peplan->phaser->R;
 
         ks_enum_epiblipsign blipsign = ks_scan_epi_verify_phaseenc_plan(&ksepi.epitrain, ksepi.current_peplan, shot);
         int post_delay = 0;
 
         if (blipsign == KS_EPI_POSBLIPS) {
          post_delay = (kyshot <= 0) ? GRAD_UPDATE_TIME : RUP_GRD((int) (ksepi_echotime_shifting_shotdelay * kyshot));
         } else if (blipsign == KS_EPI_NEGBLIPS) {
          post_delay = (kyshot <= 0) ? GRAD_UPDATE_TIME : RUP_GRD((int) (ksepi_echotime_shifting_shotdelay * (ksepi.current_peplan->phaser->R-1-kyshot)));
         }
 
         ks_scan_wait(&ksepi.pre_delay, ksepi_echotime_shifting_sumdelay - post_delay);
         ks_scan_wait(&ksepi.post_delay, post_delay);
       }
 
       if (ksinv1.params.irmode != KSINV_OFF) {
         void *args[] = {(void *) &shot}; /* pass on args via ksinv_scan_sliceloop() to ksepi_scan_coreslice() */
         int nargs = sizeof(args) / sizeof(void *);
         time += (float) ksinv_scan_sliceloop(&ks_slice_plan, ks_scan_info, passindx, &ksinv1, &ksinv2, &ksinv_filltr,
                                               (shot < 0) ? KSINV_LOOP_DUMMY : KSINV_LOOP_NORMAL, ksepi_scan_coreslice_nargs, nargs, args);
       } else {
         time += (float) ksepi_scan_sliceloop(ks_slice_plan.nslices_per_pass, volindx, passindx, shot);
       }
 
       ks_plot_slicetime_endofslicegroup(volindx < 0 ? "ksepi ghostcorr" : "ksepi shots");
 
       /* save a frame of the main sequence */
       if (shot >= 0) {
         ks_plot_tgt_addframe(&ksepi.seqctrl);
       }
 
     } /* for shot */
     ks_plot_slicetime_endofpass(volindx < 0 ? KS_PLOT_PASS_WAS_CALIBRATION : KS_PLOT_PASS_WAS_STANDARD);
   }
 
   return time; /* in [us] */
 
 } /* ksepi_scan_acqloop() */

◆ ksepi_scan_scanloop()

float ksepi_scan_scanloop ( )

Plays out all volumes and passes of a single or multi-pass scan

This function performs the entire scan and traverses through passes and volumes. For each passindx (in range [0, ks_slice_plan.npasses-1]), and volindx, ksepi_scan_acqloop() will be called to acquire all data for the current set of slices belong to the current pass (acquisition).

Return values

scantime Total scan time in [us] (float to avoid int overrange after 38 mins)

                             {
   float time = 0.0;
   int volindx, passindx;
 
   for (volindx = -ksepi_fleet - ksepi_ghostcorr; volindx < opfphases; volindx++) { /* opfphases = # volumes */
 
     if (ksepi_ghostcorr && volindx == -1) /* if ghostcorr is used it will be volume -1 */
       rspent = L_REF; /* will make zero phase encodes in ksepi_scan_coreslice() */
     else
       rspent = L_SCAN;
 
     if (opdiffuse) {
       ksepi_diffusion_scan_diffamp(&ksepi, volindx);
     }
 
     for (passindx = 0; passindx < ks_slice_plan.npasses; passindx++) {
 
       time += ksepi_scan_acqloop(passindx, volindx, ksepi_multishot_control);
 
 #ifdef IPG
       if ( !((volindx + 1 == opfphases) && (passindx + 1 == ks_slice_plan.npasses)) ) {
         GEReq_endofpass(); /* don't play last time, we rely now on  GEReq_endofpassandscan() in ksepi.e:scan() */
       }
 #endif
 
     } /* end: acqs (pass) loop */
 
   } /* end: volume loop */
 
   return time; /* in [us] */
 
 } /* ksepi_scan_scanloop() */

◆ ksepi_init_imagingoptions()

void ksepi_init_imagingoptions ( void )

Initial handling of imaging options buttons and top-level CVs at the PSD type-in page

Returns: void

                                      {
   int numopts = sizeof(sequence_iopts) / sizeof(int);
 
   psd_init_iopt_activity();
   activate_iopt_list(numopts, sequence_iopts);
   enable_iopt_list(numopts, sequence_iopts);
 
   /* Imaging option control functions (using PSD_IOPT_ZIP_512 as example):
     - Make an option unchecked and not selectable: disable_ioption(PSD_IOPT_ZIP_512)
     - Make an option checked and not selectable:   set_required_disabled_option(PSD_IOPT_ZIP_512)
     - Remove the imaging option:                   deactivate_ioption(PSD_IOPT_ZIP_512)
   */
 
   /* Do not allow 3D multislab to be selected until supported by the PSD */
   cvmax(opimode, PSD_3D);
 
   /* Button accept control */
   cvmax(opflair, OPFLAIR_GROUP); /* allow T2-FLAIR */
   cvmax(opepi, 1);
   cvdef(opepi, 1);
   cvmax(opmph, 1);
   cvmax(opdiffuse, 1);
 
   if (KS_3D_SELECTED) {
     deactivate_ioption(PSD_IOPT_IR_PREP);
   } 
 
   /* flow comp only for GE-EPI */
   if (exist(oppseq) == PSD_SE) {
     deactivate_ioption(PSD_IOPT_FLOW_COMP);
   }
 
   if (opflair) {
     deactivate_ioption(PSD_IOPT_IR_PREP);
   }
 
   if (opdiffuse) {
     deactivate_ioption(PSD_IOPT_MPH);
   }
 
 #ifdef SIM
   opepi = !KS_3D_SELECTED;
   setexist(opepi, PSD_ON);
   opirmode = PSD_OFF; /* default interleaved slices */
   setexist(opirmode, PSD_ON);
 #endif
 
   /* GERequired.e:GEReq_cvinit() sets ks_qfact (acoustic reduction) when
      ART (opsilent) has been selected. For medium/high ART, ks_qfact is set to 8/20.
      However, for EPI, the geometric distortions becomes too severe so can no
      reduce the slewrate for EPI as much (and hence the amount of acoustic reduction). 
      
      Also the SPSP RF pulse uses a gradwave that cannot be derated.
      If we use SPSP RF exc (opfat == FALSE), we set ks_qfact = 1.0.
      With opfat ks_qfact will be set by GEReq_cvinit() and the sequence will run quieter
      In all cases, the EPI readout gradients are controlled by ksepi_epiqfact */
      
   if (opsilent) {
 
     if (opfat == FALSE) { 
       /* SPectral-SPatial RF. Cannot derate excitation waveform */
       ks_qfact = 1.0; /* for all gradients except the EPI readout */
       GEReq_init_gradspecs(&loggrd, &phygrd, ks_srfact / ks_qfact);
     }
 
     if (opsilentlevel == 1) {
       /* moderate ART (small acoustic reduction) */
       ksepi_epiqfact = 3.0;
     } else {
       /* high ART (moderate acoustic reduction) */
       ksepi_epiqfact = 6.0; /* for the EPI readout */
     }
   } else {
     ksepi_epiqfact = 1.0;
   }
 
   pipure = PSD_PURE_COMPATIBLE_2; /* or maybe PSD_PURE_COMPATIBLE_1 ? */
 
 
 } /* ksepi_init_imagingoptions() */

◆ ksepi_init_UI()

STATUS ksepi_init_UI ( void )

Initial setup of user interface (UI) with default values for menus and fields

Return values

STATUS SUCCESS or FAILURE

                            {
   STATUS status;
 
   /* Slice oversampling for 3D to avoid aliasing */
   if (KS_3D_SELECTED) {
     pislblank = ksepi_kissoff_factor * exist(opslquant);
   }
 
   /* Spin or Gradient Echo EPI */
   if (exist(oppseq) == PSD_SE || exist(oppseq) == PSD_IR) {
     acq_type = TYPSPIN; /* SE, FLAIR, or Diffusion EPI */
   } else {
     acq_type = TYPGRAD; /* GRE-EPI */
   }
 
   /* force flow comp off for non-GE-EPI */
   if (acq_type != TYPGRAD) {
     cvoverride(opfcomp, FALSE, PSD_FIX_ON, PSD_EXIST_ON);
   }
 
   /* rBW */
   pircbnub = (KS_3D_SELECTED) ? 4 : 5; /* number of variable bandwidth */
   pircb2nub = 0; /* no second bandwidth option */
   cvmin(oprbw, 15.625);
   if (ksepi_rampsampling) {
     cvmax(oprbw, (KS_3D_SELECTED) ? 125 : 250);
     cvdef(oprbw, (KS_3D_SELECTED) ? 125 : 250);
     pircbval2 = 31.25;
     pircbval3 = 62.50;
     pircbval4 = 125.0;
     pircbval5 = (KS_3D_SELECTED) ? 125 : 250;
   } else {
     cvmax(oprbw, KSEPI_MAXRBW_NORAMPSAMPLING);
     cvdef(oprbw, 62.5);
     pircbval2 = 31.25;
     pircbval3 = 62.50;
     pircbval4 = 83.33;
     pircbval5 = KSEPI_MAXRBW_NORAMPSAMPLING;
   }
   if (oprbw > _oprbw.maxval) {
     /* this avoid minFOV errors for rBW = 250 when FOV < 35 cm */
     cvoverride(oprbw, KSEPI_MAXRBW_NORAMPSAMPLING, _oprbw.fixedflag, _oprbw.existflag);
   }
   oprbw = _oprbw.defval;
   pidefrbw = _oprbw.defval;
 
   /* NEX - never show. Partial Fourier in ky is done with opte = MINTE, not with NEX < 1 */
   cvdef(opnex, 1);
   opnex = _opnex.defval;
   cvmin(opnex, 1);
   cvmax(opnex, 1);
   opnex = 1;
   if (opdiffuse) {
     cvoverride(opnex, 1, PSD_FIX_OFF, PSD_EXIST_ON);
     pinexnub = 0;
   } else {
     pinexnub = 63;
   }
   pinexval2 = 1;
   pinexval3 = 1;
   pinexval4 = 1;
   pinexval5 = 1;
   pinexval6 = 1;
 
   /* FOV */
   opfov = 240;
   pifovnub = 5;
   pifovval2 = 200;
   pifovval3 = 220;
   pifovval4 = 240;
   pifovval5 = 260;
   pifovval6 = 280;
 
   /* phase FOV fraction */
   opphasefov = 1;
   piphasfovnub2 = 63;
   piphasfovval2 = 1.0;
   piphasfovval3 = 0.9;
   piphasfovval4 = 0.8;
   piphasfovval5 = 0.7;
   piphasfovval6 = 0.6;
 
   /* freq (x) resolution */
   cvmin(opxres, 16);
 
   /* phase (y) resolution */
   cvmin(opyres, 16);
 
   if (KS_3D_SELECTED) {
       /* assuming many shots for 3D */
       cvdef(opxres, 320);
       pixresnub = 63;
       pixresval2 = 192;
       pixresval3 = 256;
       pixresval4 = 288;
       pixresval5 = 320;
       pixresval6 = 384;
 
       cvdef(opyres, 320);
       piyresnub = 63;
       piyresval2 = 192;
       piyresval3 = 256;
       piyresval4 = 288;
       piyresval5 = 320;
       piyresval6 = 384;
   } else {
     cvdef(opxres, 64);
     cvdef(opyres, 64);
     if (opdiffuse) {
       pixresnub = 63;
       pixresval2 = 96;
       pixresval3 = 128;
       pixresval4 = 160;
       pixresval5 = 192;
       pixresval6 = 224;
 
       piyresnub = 63;
       piyresval2 = 96;
       piyresval3 = 128;
       piyresval4 = 160;
       piyresval5 = 192;
       piyresval6 = 224;
     } else {
       pixresnub = 63;
       pixresval2 = 32;
       pixresval3 = 64;
       pixresval4 = 96;
       pixresval5 = 128;
       pixresval6 = 160;
 
       piyresnub = 63;
       piyresval2 = 32;
       piyresval3 = 64;
       piyresval4 = 96;
       piyresval5 = 128;
       piyresval6 = 160;
     }
   }
   opxres = _opxres.defval;
   opyres = _opyres.defval;
 
 
   /* Num echoes */
   piechnub = 63;
   cvdef(opnecho, 1);
   cvmax(opnecho, 8);
   opnecho = _opnecho.defval;
   piechdefval = _opnecho.defval;
   piechval2 = 1;
   piechval3 = 2;
   piechval4 = 4;
   piechval5 = 6;
   piechval6 = 8;
 
   /* ETL */
   cvmax(opetl, 1024);
   pietlnub = 0;
 
   /* TE */
   avmaxte = 1s;
   avminte = 0;
   avminte2 = 0;
   pitetype = PSD_LABEL_TE_EFF; /* alt. PSD_LABEL_TE_EFF */
   cvdef(opte, 200ms);
   opte = _opte.defval;
   pite1nub = 63;
   pite1val2 = PSD_MINIMUMTE;
   pite1val3 = PSD_MINFULLTE;
   pite1val4 = 30ms;
   pite1val5 = 50ms;
   pite1val6 = 70ms;
 
   /* TE2 */
   /* pite2nub = 0; */
 
   /* TR */
   cvdef(optr, 2s);
   optr = _optr.defval;
   if (opfast == TRUE) {
     pitrnub = 0; /* '0': shown but greyed out (but only if opautotr = 1, otherwise TR menu is hidden) */
     cvoverride(opautotr, PSD_ON, PSD_FIX_OFF, PSD_EXIST_ON);
   } else {
     pitrnub = 6; /* '2': only one menu choice (Minimum = AutoTR) */
   }
   pitrval2 = PSD_MINIMUMTR;
   pitrval3 = 1000ms;
   pitrval4 = 2000ms;
   pitrval5 = 3000ms;
   pitrval6 = 4000ms;
 
   /* FA */
   if (acq_type == TYPSPIN) {
     cvdef(opflip, 180); /* refocusing RF: initialize with low FA to avoid gradrf complaints on load */
     pifanub = 0; /* can also be e.g. 2 to allow modification of refocusing flip angle */
     pifamode = PSD_FLIP_ANGLE_MODE_REFOCUS;
     pifaval2 = 180;
   } else {
     pifanub = 6;
     pifamode = PSD_FLIP_ANGLE_MODE_EXCITE;
     cvdef(opflip, 10);
     pifaval2 = 10;
     pifaval3 = 15;
     pifaval4 = 20;
     pifaval5 = 30;
     pifaval6 = 90;
   }
   opflip = _opflip.defval;
 
 
   /* slice thickness */
   pistnub = 5;
   if (!KS_3D_SELECTED) {
     cvdef(opslthick, 4);
     pistval2 = 3;
     pistval3 = 4;
     pistval4 = 5;
     pistval5 = 6;
     pistval6 = 10;
   } else {
     cvdef(opslthick, 2);
     pistval2 = 1.50;
     pistval3 = 1.75;
     pistval4 = 2.00;
     pistval5 = 2.25;
     pistval6 = 2.50;
   }
   opslthick = _opslthick.defval;
 
   /* slice spacing */
   cvdef(opslspace, 0);
   opslspace = _opslspace.defval;
   piisil = PSD_ON;
   if (!KS_3D_SELECTED) {
     piisnub = 4;
     piisval2 = 0;
     piisval3 = 0.5;
     piisval4 = 1;
     piisval5 = 4;
     piisval6 = 20;
   } else { /* change these to do overlaps */
     piisnub = 0;
     piisval2 = 0;
   }
 
   /* default # of slices */
   cvdef(opslquant, 30);
 
   /* 3D slice settings */
   if (KS_3D_SELECTED) {/* PSD_3D (=2) or PSD_3DM (=6) */
 
     if (opimode == PSD_3DM) {
       return ks_error("ksepi: 3D multislab mode not supported");
     }
 
     if (acq_type == TYPSPIN) {
       return ks_error("ksepi: 3D spin echo epi not supported");
     }
 
     pimultislab = 0; /* 0: forces only single slab, 1: allow multi-slab */
     pilocnub = 4;
     pilocval2 = 32;
     pilocval3 = 64;
     pilocval4 = 128;
     /* opslquant = #slices in slab. opvquant = #slabs */
     cvdef(opslquant, 32);
   }
 
   /* Multi phase (i.e. multi volumes) */
   if (opmph) {
     pimphscrn = 1;   /* display Multi-Phase Parameter screen */
     pifphasenub = 6;
     pifphaseval2 = 10;
     pifphaseval3 = 20;
     pifphaseval4 = 50;
     pifphaseval5 = 100;
     pifphaseval6 = 200;
     pisldelnub = 0;
     /*
     pisldelval3 = 1s;
     pisldelval4 = 2s;
     pisldelval5 = 5s;
     pisldelval6 = 10s;
     */
     piacqnub = 0;
     setexist(opacqo, 1);
     pihrepnub = 0;  /* no XRR gating */
   } else {
     if (!opdiffuse) {
       cvoverride(opfphases, 1, PSD_FIX_OFF, PSD_EXIST_OFF);
     }
     pimphscrn = 0;   /* do not display the Multi-Phase Parameter screen */
   }
 
 
   /* Prescan buttons (autoshim). c.f. epic.h */
   pipscoptnub = 1; /* Bit map of number of Prescan option buttons. 0=none, 1=autoshim, 2=phase corr */
 
   /* opuser0: show GIT revision (GITSHA) using REV variable from the Imakefile */
 #ifdef REV
   char userstr[100];
   sprintf(userstr, "PSD version: %s", REV);
   cvmod(opuser0, 0, 0, 0, userstr, 0, " ");
   piuset |= use0;
 #endif
 
   /* opuser1: Number of overscans (extra kylines) for partial Fourier */
   cvmod(opuser1, _ksepi_kynover.minval, _ksepi_kynover.maxval, _ksepi_kynover.defval, _ksepi_kynover.descr, 0, " ");
   opuser1 = _ksepi_kynover.defval;
   piuset |= use1;
 
   cvmod(opuser2, _ksepi_blipsign.minval, _ksepi_blipsign.maxval, _ksepi_blipsign.defval, _ksepi_blipsign.descr, 0, " ");
   opuser2 = _ksepi_blipsign.defval;
   piuset |= use2;
 
 
 
   /* enum {KSEPI_MULTISHOT_OFF=0,KSEPI_MULTISHOT_ALLVOLS=1,KESPI_MULTISHOT_1STVOL=2, KSEPI_MULTISHOT_B0VOLS=3 */
   if (KS_3D_SELECTED) {
     piuset &= ~use5;
     cvdef(ksepi_multishot_control, 0);
   } else {
     piuset |= use5;
     if (opdiffuse) {
       cvdef(ksepi_multishot_control, 3);
       cvdesc(ksepi_multishot_control, "0:PI 1:All MulShot 2:1stMulShot 3:b0MulShot");
     } else {
       cvdef(ksepi_multishot_control, 2);
       cvdesc(ksepi_multishot_control, "0:PI 1:All MulShot 2:1stMulShot");
     }
   }
   cvmod(opuser5, _ksepi_multishot_control.minval, _ksepi_multishot_control.maxval, _ksepi_multishot_control.defval, _ksepi_multishot_control.descr, 0, " ");
   opuser5 = (float) _ksepi_multishot_control.defval;
 
   /* OFFLINE_DIFFRETURN_ALL = 0, OFFLINE_DIFFRETURN_ACQUIRED = 1, OFFLINE_DIFFRETURN_B0 = 2, OFFLINE_DIFFRETURN_MEANDWI = 4, OFFLINE_DIFFRETURN_MEANADC = 8, OFFLINE_DIFFRETURN_EXPATT = 16, OFFLINE_DIFFRETURN_FA = 32, OFFLINE_DIFFRETURN_CFA = 64; */
   cvmod(opuser6, _ksepi_diffusion_returnmode.minval, _ksepi_diffusion_returnmode.maxval, _ksepi_diffusion_returnmode.defval, _ksepi_diffusion_returnmode.descr, 0, " ");
   opuser6 = (float) _ksepi_diffusion_returnmode.defval;
   if (opdiffuse) {
     piuset |= use6;
   } else {
     piuset &= ~use6;
   }
 
   cvmod(opuser7, _ksepi_swi_returnmode.minval, _ksepi_swi_returnmode.maxval, _ksepi_swi_returnmode.defval, _ksepi_swi_returnmode.descr, 0, " ");
   opuser7 = (float) _ksepi_swi_returnmode.defval;
   if (oppseq != PSD_SE) { /* show for GE variants (PSD_GE, PSD_SPGR, ...) */
    piuset |= use7;
   } else {
    piuset &= ~use7;
    cvoverride(ksepi_swi_returnmode, 0, PSD_FIX_OFF, PSD_EXIST_OFF);
   }
 
   /* make FLEET volume for GRAPPA calibration  */
   _ksepi_fleet.defval = !KS_3D_SELECTED; /* Default off for 3D */
   cvmod(opuser8, _ksepi_fleet.minval, _ksepi_fleet.maxval, _ksepi_fleet.defval, _ksepi_fleet.descr, 0, " ");
   opuser8 = (float) _ksepi_fleet.defval;
   piuset |= use8;
 
   /* Number of phase reference lines for ghost correction per shot */
   cvdef(ksepi_reflines, 0);
   ksepi_reflines = _ksepi_reflines.defval;
 
   cvmod(opuser9, _ksepi_reflines.minval, _ksepi_reflines.maxval, _ksepi_reflines.defval, _ksepi_reflines.descr, 0, " ");
   opuser9 = (float) _ksepi_reflines.defval;
   piuset |= use9;
 
   if (KS_3D_SELECTED) {
     piuset |= use12;
     cvdef(ksepi_rf3Dopt, 1);
   } else {
     piuset &= ~use12;
     cvdef(ksepi_rf3Dopt, 0);
   }
   ksepi_rf3Dopt = _ksepi_rf3Dopt.defval;
   cvmod(opuser12, _ksepi_rf3Dopt.minval, _ksepi_rf3Dopt.maxval, _ksepi_rf3Dopt.defval, "Choose 3D RF", 0, " ");
   opuser12 = (float) _ksepi_rf3Dopt.defval;
 
   if (KS_3D_SELECTED) {
     cvmod(opuser15, _ksepi_kz_nacslines.minval, _ksepi_kz_nacslines.maxval, _ksepi_kz_nacslines.defval, _ksepi_kz_nacslines.descr, 0, " ");
     opuser15 = (int) _ksepi_kz_nacslines.defval;
     piuset |= use15;
   } else {
     piuset &= ~use15;
   }
 
   /*
      Reserved opusers:
      -----------------
      ksepi_diffusion_predownload_setrecon(): opuser20-25 (needed by GE's recon)
      ksepi_eval_inversion(): opuser26-29
      GE reserves: opuser36-48 (epic.h)
    */
 
 
   /* Acceleration menu (max accel = 4). But we don't show ARC for 2D */
   GEReq_init_accelUI(KS_ACCELMENU_INT, 4);
 
   /* multi-shot button (see also ksepi_eval_UI()) */
   if (opdiffuse) {
     pishotnub = 0;
   } else {
     pishotnub = 63;
   }
   if (KS_3D_SELECTED) {
     pishotval2 = 8;
     pishotval3 = 12;
     pishotval4 = 16;
     pishotval5 = 24;
     pishotval6 = 32;
     cvdef(opnshots, 16);
 } else {
     pishotval2 = 1;
     pishotval3 = 2;
     pishotval4 = 4;
     pishotval5 = 8;
     pishotval6 = 16;
     cvdef(opnshots, 1);
   }
   cvmin(opnshots, 1);
   cvmax(opnshots, 512);
   opnshots = _opnshots.defval;
 
   /* Make R/L freq encoding attempts (a la epi2.e) */
   if ((TX_COIL_LOCAL == getTxCoilType() && (exist(opplane) == PSD_AXIAL || exist(opplane)== PSD_COR) ) ||
       (TX_COIL_LOCAL == getTxCoilType() &&  exist(opplane) == PSD_OBL && existcv(opplane) && (exist(opobplane) == PSD_AXIAL || exist(opobplane) == PSD_COR) )) {
       piswapfc = 1;
   } else {
       piswapfc = 0;
   }
 
 
 
   /* Diffusion init */
   status = ksepi_diffusion_init_UI();
   if (status != SUCCESS) return status;
 
   return SUCCESS;
 
 } /* ksepi_init_UI() */

◆ ksepi_eval_UI()

STATUS ksepi_eval_UI ( )

Gets the current UI and checks for valid inputs

Return values

STATUS SUCCESS or FAILURE

                        {
   STATUS status;
 
   if (ksepi_init_UI() == FAILURE)
     return FAILURE;
 
   /*** Copy UserCVs to human readable CVs ***/
   if (existcv(opautote) && opautote == PSD_MINTE) {
     ksepi_kynover = (int) opuser1;
     if (ksepi_kynover < _ksepi_kynover.minval || ksepi_kynover > _ksepi_kynover.maxval)
       return ks_error("'#extralines for minTE' is out of range");
   }
 
   ksepi_blipsign = (int) opuser2;
   if (ksepi_blipsign != KS_EPI_POSBLIPS && ksepi_blipsign != KS_EPI_NEGBLIPS) {
     return ks_error("The EPI blip sign must be either +1 or -1"); /* User error */
   }
 
   /* ksepi_ky_R = 1 means that k-space is fully sampled over opnshots TR
      ksepi_ky_R = opnshots means that k-space is sampled once with undersampling factor of opnshots
      See also ksepi_pg()->ks_phaseencoding_generate_epi() where multiple phase encoding plans are set up. */
  
   cvoverride(ksepi_ky_R, (oparc) ? ((int) opaccel_ph_stride) : 1, PSD_FIX_ON, PSD_EXIST_ON);
 
   if (opdiffuse) {
     cvoverride(opnshots, ksepi_ky_R, PSD_FIX_ON, PSD_EXIST_ON); /* Shots and undersampling must be the same for diffusion */
   } 
 
   if (existcv(opnshots) && (opnshots > 1 && (opnshots % ksepi_ky_R != 0))) {
     return ks_error("R must be an integer factor of opnshots"); /* User error */
   }
 
   /* Reserved opusers:
      -----------------
      ksepi_diffusion_predownload_setrecon(): opuser20-25 (needed by GE's recon)
      ksepi_eval_inversion(): opuser26-29
      GE reserves: opuser36-48 (epic.h)
   */
 
   /* Multi-shot  */
 
   ksepi_multishot_control = (int) (KS_3D_SELECTED) ? 0 : opuser5;
   if (ksepi_multishot_control < _ksepi_multishot_control.minval || ksepi_multishot_control > _ksepi_multishot_control.maxval) {
     return ks_error("multishot control (CV5) must be in range [%d,%d]", _ksepi_multishot_control.minval, _ksepi_multishot_control.maxval);
   }
   cvoverride(opasset, FALSE, _opasset.fixedflag, _opasset.existflag); /* force asset off, but keep exist/fixed status */
   piechnub = 63;
 
   ksepi_diffusion_returnmode = (int) opuser6;
 
   /* Don't do the extra ghost correction volume (integrated refscan) if ETL = 1 */
   if (ksepi.epitrain.etl == 1) {
     ksepi_ghostcorr = FALSE;
   } else {
     ksepi_ghostcorr = TRUE;
   }
 
   /* Diffusion eval */
   status = ksepi_diffusion_eval_UI();
   if (status != SUCCESS) return status;
 
   ksepi_swi_returnmode = (int) opuser7;
 
   ksepi_fleet = (int) opuser8;
   ksepi_reflines = (int) opuser9;
 
   ksepi_rf3Dopt = (int) opuser12;
 
   ksepi_kz_nacslines = (int) opuser15;
 
   return SUCCESS;
 
 } /* ksepi_eval_UI() */

◆ ksepi_eval_setuprf_3dexc()

STATUS ksepi_eval_setuprf_3dexc	(	KS_SELRF *	selrfexc,
		int	rf3Dopt
	)

                                                                  {
 
 
     selrfexc->rf = spsp_ss30260334; /* 3T SPSP */
     selrfexc->gradwave = spsp_ss30260334_gz; /* normalized to 1 G/cm */
 
     if (rf3Dopt > 0) {
 
       if (exist(opslquant) * exist(opslthick) >= 150) {
 
         /* 150 mm pulses goes here */
 
         switch (rf3Dopt) {
 
           case 1:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw4_lin_lin; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw4_lin_lin_gz; /* normalized to 1 G/cm */
           break;
 
           case 2:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw4_lin_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw4_lin_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 3:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw5_lin_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw5_lin_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 4:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw4_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw4_min_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 5:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw5_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw5_min_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 6:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw6_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw6_min_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 7:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw4_max_max; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw4_max_max_gz; /* normalized to 1 G/cm */
           break;
 
           case 8:
             selrfexc->rf       = exc_SPSP3D_150mm_stbw10_etbw5_max_max; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_150mm_stbw10_etbw5_max_max_gz; /* normalized to 1 G/cm */
           break;
 
           default:
             return ks_error("%s: ksepi_rf3Dopt = %d is out of range", __FUNCTION__, ksepi_rf3Dopt);
           break;
         }
 
       } else if (exist(opslquant) * exist(opslthick) >= 40) {
 
         /* 40 mm pulses goes here */
           switch(rf3Dopt) {
 
           case 1:
             selrfexc->rf       = exc_SPSP3D_40mm_stbw4_etbw5_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_40mm_stbw4_etbw5_min_min_gz; /* normalized to 1 G/cm */
           break;
 
           case 2:
             selrfexc->rf       = exc_SPSP3D_40mm_stbw4_etbw6_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_40mm_stbw4_etbw6_min_min_gz; /* normalized to 1 G/cm */
           break;
 
           default: /* same as case 2 for now. Don't want to throw an error when slab is lower than 150 mm and rf3Dopt > 2 */
             selrfexc->rf       = exc_SPSP3D_40mm_stbw4_etbw6_min_min; /* 3T SPSP */
             selrfexc->gradwave = exc_SPSP3D_40mm_stbw4_etbw6_min_min_gz; /* normalized to 1 G/cm */
           break;
           }
 
       } /* >= 40 mm */
 
     } /* rf3Dopt > 0 */
 
     char tmpstr[KS_DESCRIPTION_LENGTH+20];
     sprintf(tmpstr, "Choose 3D RF [%s]", selrfexc->rf.designinfo);
     cvdesc(opuser12, tmpstr);
 
   return SUCCESS;
 }

◆ ksepi_eval_setuprf()

STATUS ksepi_eval_setuprf ( )

                             {
 
   /* selective RF excitation */
   if (opfat || ksepi_fse90 == TRUE) {
     ksepi.selrfexc.rf = exc_fse90; /* KSFoundation_GERF.h */
     ks_init_wave(&ksepi.selrfexc.gradwave); /* clear gradwave */
   } else {
     if (cffield == 30000) {
       if (KS_3D_SELECTED) {
         if (ksepi_eval_setuprf_3dexc(&ksepi.selrfexc, ksepi_rf3Dopt) == FAILURE)
           return FAILURE;
       } else {
         /* In 2D always use the standard GE pulse */
         ksepi.selrfexc.rf = spsp_ss30260334; /* 3T SPSP */
         ksepi.selrfexc.gradwave = spsp_ss30260334_gz; /* normalized to 1 G/cm */
       }
     } else {
       ksepi.selrfexc.rf = spsp_ss1528822; /* 1.5T SPSP */
       ksepi.selrfexc.gradwave = spsp_ss1528822_gz; /* normalized to 1 G/cm */
     }
   } /* RF Excitation */
 
   if (acq_type == TYPSPIN)
     ksepi.selrfexc.rf.flip = 90.0; /* always 90 FA for SE-EPI */
   else
     ksepi.selrfexc.rf.flip = opflip; /* variable FA for GE-EPI */
 
   if (KS_3D_SELECTED) {
     cvoverride(opvthick, exist(opslquant) * exist(opslthick), _opslquant.fixedflag, existcv(opslquant));
     ksepi_excthickness = (exist(opslquant) - 2 * pislblank) * exist(opslthick);
   } else {
     ksepi_excthickness = opslthick;
   }
 
   /* Don't oversize slices for 3D */
   ksepi_gscalerfexc = (KS_3D_SELECTED) ? 1.0 : 0.9;
   ksepi_gscalerfref = (KS_3D_SELECTED) ? 1.0 : 0.9;
   
   ksepi.selrfexc.slthick = ksepi_excthickness / ksepi_gscalerfexc;
 
 
   if (ks_eval_selrf1p(&ksepi.selrfexc, "rfexc") == FAILURE) {
     if (opfat || opslthick >= 3.0) {
       return FAILURE;
     } else {
       /* override the error message from ks_eval_selrf1p() for SPSP and thin slices, to guide the operator to run the sequence
       with a fat sat pulse and a regular 90 pulse  */
       return ks_error("ks_eval_selrf1p(rfexc): Too small slice thickness. Try FatSat pulse");
     }
   }
     
 
   /* selective RF refocusing */
   if (acq_type == TYPSPIN) {
     ksepi.selrfref.rf = ref_se1b4;
     ksepi.selrfref.rf.flip = opflip; /* since pifamode = PSD_FLIP_ANGLE_MODE_REFOCUS when TYPSPIN */
     ksepi.selrfref.slthick = ksepi_excthickness / ksepi_gscalerfref;
     ksepi.selrfref.crusherscale = ksepi_crusherscale;
 
     if (ks_eval_selrf1p(&ksepi.selrfref, "rfref") == FAILURE)
       return FAILURE;
   } else {
     ks_init_selrf(&ksepi.selrfref); /* GE-EPI: reset to default values (incl. zero .duration) */
   }
 
   /* selective RF refocusing with diffusion and opdualspinecho */
   if (acq_type == TYPSPIN && opdiffuse && opdualspinecho) {
     ksepi.selrfref2.rf = ref_se1b4;
     ksepi.selrfref2.rf.flip = opflip; /* since pifamode = PSD_FLIP_ANGLE_MODE_REFOCUS when TYPSPIN */
     ksepi.selrfref2.slthick = ksepi_excthickness / ksepi_gscalerfref;
     ksepi.selrfref2.crusherscale = ksepi_crusherscale * ksepi_diffusion_2ndcrushfact; /* ksepi_diffusion_2ndcrushfact times bigger crushers to avoid stimulated echoes */
 
     if (ks_eval_selrf1p(&ksepi.selrfref2, "rfref2") == FAILURE)
       return FAILURE;
   } else {
     ks_init_selrf(&ksepi.selrfref2); /* Not opdualspinecho diffusion: reset to default values (incl. zero .duration) */
   }
 
   return SUCCESS;
 
 } /* ksepi_eval_setuprf() */

◆ ksepi_eval_setupfleet()

STATUS ksepi_eval_setupfleet ( )

                                {
 
   ksepi_fleetseq.selrfexc = ksepi.selrfexc;
   ksepi_fleetseq.selrfexc.rf.flip = ksepi_fleet_flip;
   if (ks_eval_selrf1p(&ksepi_fleetseq.selrfexc, "fleetrfexc") == FAILURE)
     return FAILURE;
 
   /* echo time shifting */
   ks_init_wait(&ksepi_fleetseq.pre_delay);
   ks_init_wait(&ksepi_fleetseq.post_delay);
   if (ksepi_echotime_shifting == TRUE) {
     /*** Set up a pair of wait objects that are used to shift back the RF up to the echospacing ***/
     if (ks_eval_wait(&ksepi_fleetseq.pre_delay,"ksepi_fleet_wait_pre", GRAD_UPDATE_TIME) == FAILURE) {
       return FAILURE;
     }
     if (ks_eval_wait(&ksepi_fleetseq.post_delay,"ksepi_fleet_wait_post", ksepi_echotime_shifting_sumdelay - GRAD_UPDATE_TIME) == FAILURE) {
       return FAILURE;
     }
   }
 
   ksepi_fleetseq.epitrain = ksepi.epitrain;
   ksepi_fleetseq.epitrain.blipphaser.res = IMin(2, 
                                                 RUP_FACTOR((int) ksepi_fleet_num_ky, 2), /* round up (RUP) to nearest multiple of 2 */
                                                 (ksepi.epitrain.blipphaser.nover != 0) ? (ksepi.epitrain.blipphaser.res/2 + abs(ksepi.epitrain.blipphaser.nover)) : ksepi.epitrain.blipphaser.res);
   ksepi_fleetseq.epitrain.blipphaser.nover = 0; /* no partial Fourier for FLEET */
   
   if (KS_3D_SELECTED) { /* PSD_3D or PSD_3DM */
     ksepi_fleetseq.epitrain.zphaser.res = IMax(2, 1, IMin(2, ksepi_fleet_num_kz, opslquant));
   } else {
     ksepi_fleetseq.epitrain.zphaser.res = KS_NOTSET;
   }
   
   if (ks_eval_epi(&ksepi_fleetseq.epitrain, "epifleet", ks_qfact) == FAILURE)
     return FAILURE;
 
   ksepi_fleetseq.spoiler.area = ksepi_spoilerarea;
   if (ks_eval_trap(&ksepi_fleetseq.spoiler, "fleetspoiler") == FAILURE)
     return FAILURE;
 
   ks_init_seqcontrol(&ksepi_fleetseq.seqctrl);
   strcpy(ksepi_fleetseq.seqctrl.description, "ksepifleet");
 
   return SUCCESS;
 }

◆ ksepi_eval_setupobjects()

STATUS ksepi_eval_setupobjects ( )

Sets up all sequence objects for the main sequence module (KSEPI_SEQUENCE ksepi)

Return values

STATUS SUCCESS or FAILURE

                                  {
 
   /* All RF related setup in separate function */
   if (ksepi_eval_setuprf() == FAILURE)
     return FAILURE;
 
  
   /* EPI readout */
   ksepi.epitrain.read_spacing = ksepi_readlobegap;
   ksepi.epitrain.read.acq.rbw = oprbw;
   ksepi.epitrain.read.fov = opfov;
   ksepi.epitrain.read.res = RUP_FACTOR(opxres, 2); /* round up (RUP) to nearest multiple of 2 */
   ksepi.epitrain.read.rampsampling = ksepi_rampsampling;
   ksepi.epitrain.read.nover = 0; /* never partial Fourier in kx for EPI */
 
   ksepi.epitrain.blipphaser.fov = opfov * opphasefov;
   ksepi.epitrain.blipphaser.res = RUP_FACTOR((int) (opyres * opphasefov), 2); /* round up (RUP) to nearest multiple of 2 */
 
   /* upsample to nearest power of 2 for res up to 256. For higher matrix sizes, use native res
      KSFoundation.h: {KS_IMSIZE_NATIVE, KS_IMSIZE_POW2, KS_IMSIZE_MIN256} */
   if (ksepi.epitrain.read.res < 256 && ksepi.epitrain.blipphaser.res < 256) {
     ksepi_imsize = KS_IMSIZE_POW2;
   } else {
     ksepi_imsize = KS_IMSIZE_NATIVE;
   }
 
   if (opautote == PSD_MINTE) /* partial Fourier in ky */
     ksepi.epitrain.blipphaser.nover = ksepi_kynover;
   else
     ksepi.epitrain.blipphaser.nover = 0;
 
   if (opasset == ASSET_SCAN) {
     /* ASSET acceleration, without acs lines (since 2nd arg = 0) */
     if (ks_eval_phaser_setaccel(&ksepi.epitrain.blipphaser, 0, opaccel_ph_stride) == FAILURE)
       return FAILURE;
   } else {
     /* R is used as multishot if not ASSET has been selected */
     ksepi.epitrain.blipphaser.R = opnshots; /* using multi-shot to accelerate EPI readout */
     ksepi.epitrain.blipphaser.nacslines = 0; /* never have acs lines for EPI */
   }
 
   /* z phase encoding gradient for the 3D case (one zphase enc. per TR, not real 3D EPI) */
   if (KS_3D_SELECTED) { /* PSD_3D or PSD_3DM */
     ksepi_kz_R = opaccel_sl_stride;
     ksepi.epitrain.zphaser.fov = opvthick;
     ksepi.epitrain.zphaser.res = IMax(2, 1, opslquant);
     ksepi.epitrain.zphaser.nover = IMin(2, ksepi_kznover, ksepi.epitrain.zphaser.res/2);
     ksepi.epitrain.zphaser.R = ksepi_kz_R;
     ksepi.epitrain.zphaser.nacslines = ksepi_kz_nacslines;
   } else {
     ksepi.epitrain.zphaser.res = KS_NOTSET; /* ks_eval_epi will clear zphaser if res <= 1 */
   }
 
   if (ks_eval_epi(&ksepi.epitrain, "epi", ksepi_epiqfact) == FAILURE) {
     return FAILURE;
   }
 
   /* echo time shifting */
   ks_init_wait(&ksepi.pre_delay);
   ks_init_wait(&ksepi.post_delay);
 
   if (ksepi_echotime_shifting == TRUE) {
     /*** Set up a pair of wait objects that are used to shift back the RF up to the echospacing ***/
     ksepi_echotime_shifting_shotdelay = ksepi.epitrain.read.grad.duration/ksepi.epitrain.blipphaser.R;
     ksepi_echotime_shifting_sumdelay = RUP_GRD((int) (ksepi_echotime_shifting_shotdelay * (ksepi.epitrain.blipphaser.R-1))) + GRAD_UPDATE_TIME;
     if (ks_eval_wait(&ksepi.pre_delay,"ksepi_wait_pre", GRAD_UPDATE_TIME) == FAILURE) {
       return FAILURE;
     }
     if (ks_eval_wait(&ksepi.post_delay,"ksepi_wait_post", ksepi_echotime_shifting_sumdelay - GRAD_UPDATE_TIME) == FAILURE) {
       return FAILURE;
     }
   }
 
   if (ksepi_reflines > 0) {
     ksepi.dynreftrain = ksepi.epitrain;
     ksepi.dynreftrain.blipphaser.nover = 0;
     ksepi.dynreftrain.blipphaser.res = ksepi_reflines * ksepi.dynreftrain.blipphaser.R;
 
     ksepi.dynreftrain.zphaser.res = KS_NOTSET; /* disable zphaser for reflines */
 
    if (ks_eval_epi(&ksepi.dynreftrain, "epireflines", ks_qfact) == FAILURE) {
       return FAILURE;
     }
     ks_init_phaser(&ksepi.dynreftrain.blipphaser); /* disable blipphaser for reflines */ 
     ks_init_trap(&ksepi.dynreftrain.blip); /* disable blips for reflines */
   }
   else {
     ks_init_epi(&ksepi.dynreftrain);
   }
 
   /* Flow comp */
   ks_init_trap(&ksepi.fcompphase);
   ks_init_trap(&ksepi.fcompslice);
 
   if (opfcomp == TRUE) {
 
     if (ksepi_fcy) {
       /* Y: Need two extra phase gradients for flowcomp */
       if (ksepi_eval_flowcomp_phase(&ksepi.fcompphase, &ksepi.epitrain, "fcompphase") == FAILURE)
         return FAILURE;
     }
 
     if (ksepi_fcz) {
       /* Z: Add second z rephaser to complete 0th and 1st moment nulling of slice selection */
       ksepi.fcompslice.area = -ksepi.selrfexc.postgrad.area;
       if (ks_eval_trap(&ksepi.fcompslice, "fcompslice2") == FAILURE)
         return FAILURE;   
 
       /* Z: Now, make normal z rephaser twice as large */
       ksepi.selrfexc.postgrad.area *= 2;
       if (ks_eval_trap(&ksepi.selrfexc.postgrad, "rfexc.reph_fc1") == FAILURE)
         return FAILURE;
     }
 
   } /* opfcomp */
 
 
 
   /* It is useful to be able to see the current echo spacing in DisplayCV to determine distortion levels etc */
   cvoverride(ksepi_esp, ksepi.epitrain.read.grad.duration + ksepi.epitrain.read_spacing, PSD_FIX_ON, PSD_EXIST_ON);
 
   /* for consistency, set opetl to the actual one for the EPI train even though ETL menu should never be visible for EPI */
   cvoverride(opetl, ksepi.epitrain.etl, PSD_FIX_ON, PSD_EXIST_ON);
 
 
   /* protect against too long sequence. It appears that opnecho * ksepi.epitrain.etl cannot be >= 1024 */
   if (ksepi.epitrain.etl * opnecho >= 1024)
     return ks_error("# readouts >= 1024. Please reduce echoes, phase res. or increase NumShots");
 
   /* post-read ksepi.spoiler */
   ksepi.spoiler.area = ksepi_spoilerarea;
   if (ks_eval_trap(&ksepi.spoiler, "spoiler") == FAILURE)
     return FAILURE;
 
   /* diffusion weighting */
   /* set up the diffusion gradient objects in 'ksepi'. If opdiffuse == FALSE,
     this function will reset the diffusion objects */
   if (ksepi_diffusion_eval_gradients_TE(&ksepi) == FAILURE)
       return FAILURE;
 
 
   /* init seqctrl */
   ks_init_seqcontrol(&ksepi.seqctrl);
   strcpy(ksepi.seqctrl.description, "ksepimain");
 
   /* Setup FLEET sequence */
   if (ksepi_eval_setupfleet() == FAILURE)
     return FAILURE;
 
   return SUCCESS;
 
 } /* ksepi_eval_setupobjects() */

◆ ksepi_eval_TErange()

STATUS ksepi_eval_TErange ( )

Sets the min/max TE based on the durations of the sequence objects in KSEPI_SEQUENCE (ksepi)

This function handles the TE range for SE-EPI, GE-EPI and DW-EPI (opdiffuse).

Multiple EPI trains (opnecho > 1) are supported Time between the EPI readouts is controlled using ksepi_echogap, yielding a ksepi_interechotime variable used in ksepi_pg().

N.B.: The minTE (avminte) and maxTE (avmaxte) ensures TE (opte) to be in the valid range for this pulse sequence to be set up in ksepi_pg(). If the pulse sequence design changes in ksepi_pg(), by adding/modifying/removing sequence objects in a way that affects the intended TE, this function needs to be updated too.

Return values

STATUS SUCCESS or FAILURE

                             {
   int selrfend, min90_180, min180_echo;
 
   /* RF center to RF end */
   selrfend = ksepi.selrfexc.rf.iso2end + KS_RFSSP_POSTTIME + ksepi.selrfexc.grad.ramptime;
 
   if (acq_type == TYPSPIN) {
 
     /* minimum TE: Spin-Echo EPI case (also diffusion) */
 
     /*** minimum time needed between RF exc center to RF ref center ***/
 
     /* RF center to rephaser end */
     min90_180 = selrfend + ksepi.selrfexc.postgrad.duration;
     if (ksepi_slicecheck == FALSE) { /* reflines dephaser may overlap with selrf rephaser unless slicecheck mode */
       min90_180 -= IMin(2, ksepi.dynreftrain.readphaser.duration, ksepi.selrfexc.postgrad.duration);
     }
     min90_180 += ksepi.dynreftrain.duration; /* end of reftrain */
     
     if (opdiffuse) {
       min90_180 += ksepi.diffgrad.duration;
     } else if (ksepi_slicecheck == FALSE) {
       min90_180 -= IMin(2, ksepi.dynreftrain.readphaser.duration,
                            ksepi.selrfref.pregrad.duration); /* reflines rephaser and selrefrf dephaser may overlap */
     }
     min90_180 += ksepi.selrfref.pregrad.duration + KS_RFSSP_PRETIME + ksepi.selrfref.grad.ramptime + ksepi.selrfref.rf.start2iso;
 
     /*** minimum time needed between RF ref center and echo center (using selrfref or selrfref2 (opdualspinecho) ***/
     min180_echo = ksepi.diffgrad.duration; /* zero if not opdiffuse  */
     min180_echo += ksepi.epitrain.time2center;
 
     if (ksepi_echotime_shifting == TRUE) {
       min180_echo += GRAD_UPDATE_TIME;
     }
 
     if (opdiffuse && opdualspinecho) {
       min180_echo += ksepi.selrfref2.rf.iso2end + ksepi.selrfref2.grad.ramptime + KS_RFSSP_POSTTIME + ksepi.selrfref2.postgrad.duration;
 
       /* minimum TE is 4x the biggest of the two */
       avminte = IMax(2, min90_180, min180_echo) * 4;
 
       /* Also check that the middle two diffusion gradients (diffgrad2) fits.
          There should be a time corresponding to TE/2 between the two 180 pulses for opdualspinecho, and within this time two instances
          of ksepi.diffgrad2 must be possible to fit in (2nd and 3rd diffusion gradient) */
       int avail_time = (avminte/2);
       avail_time -= ksepi.selrfref.rf.iso2end + ksepi.selrfref.grad.ramptime + KS_RFSSP_POSTTIME + ksepi.selrfref.postgrad.duration; /* right crusher for 1st 180 */
       avail_time -= ksepi.selrfref2.pregrad.duration + KS_RFSSP_PRETIME + ksepi.selrfref2.grad.ramptime + ksepi.selrfref2.rf.start2iso; /* left crusher for 2nd 180 */
       if (ksepi.diffgrad2.duration * 2 > avail_time) {
        return ks_error("%s: DualSE diffusion - not enough space for 'diffgrad2'", __FUNCTION__);
       }
 
     } else {
       min180_echo += ksepi.selrfref.rf.iso2end + ksepi.selrfref.grad.ramptime + KS_RFSSP_POSTTIME + ksepi.selrfref.postgrad.duration;
 
       /* minimum TE is 2x the biggest of the two */
       avminte = IMax(2, min90_180, min180_echo) * 2;
     }
 
   } else { /* GE-EPI */
 
     avminte = selrfend;
 
     if (ksepi_reflines > 0) {
       /* transports between selrf and reflines readout: */
       if (ksepi_slicecheck) {
         avminte += ksepi.selrfexc.postgrad.duration + ksepi.fcompslice.duration + ksepi.dynreftrain.readphaser.duration; /* Z */
       } else {
         avminte += IMax(2, ksepi.dynreftrain.readphaser.duration, /* X */
                            ksepi.selrfexc.postgrad.duration + ksepi.fcompslice.duration) /* Z */;
       }
       /* reflines readout: */
       avminte += ksepi.dynreftrain.duration - 2 * ksepi.dynreftrain.readphaser.duration;
       /* transports between reflines readout and main epi readout: */
       avminte += IMax(3, ksepi.dynreftrain.readphaser.duration + ksepi.epitrain.readphaser.duration, /* X */
                          2 * ksepi.fcompphase.duration + ksepi.epitrain.blipphaser.grad.duration, /* Y */
                          ksepi.epitrain.zphaser.grad.duration) /* Z */;
     } else { /* no reflines */
       /* transports between selrf and main epi readout: */
       if (ksepi_slicecheck) {
         avminte += IMax(3, ksepi.epitrain.zphaser.grad.duration, /* X */
                          2 * ksepi.fcompphase.duration + ksepi.epitrain.blipphaser.grad.duration, /* Y */
                          ksepi.selrfexc.postgrad.duration + ksepi.fcompslice.duration + ksepi.epitrain.readphaser.duration) /* Z */;
       } else {
         avminte += IMax(3, ksepi.epitrain.readphaser.duration, /* X */
                          2 * ksepi.fcompphase.duration + ksepi.epitrain.blipphaser.grad.duration, /* Y */
                          ksepi.selrfexc.postgrad.duration + ksepi.fcompslice.duration + ksepi.epitrain.zphaser.grad.duration) /* Z */;
       }
     }
 
     /* start of EPI readout */
     avminte -= IMax(3, ksepi.epitrain.readphaser.duration, /* X */
                        ksepi.epitrain.blipphaser.grad.duration, /* Y */
                        ksepi.epitrain.zphaser.grad.duration) /* Z */;
     /* start of EPI train */
     avminte += ksepi.epitrain.time2center; /* minimum TE ! */
 
     if (ksepi_echotime_shifting == TRUE) {
       avminte += GRAD_UPDATE_TIME;
     }
   }
 
   avminte += GRAD_UPDATE_TIME * 2; /* 8us extra margin */
   avminte = RUP_FACTOR(avminte, 8); /* round up to make time divisible by 8us */
 
   avmaxte = avminte; /* initialization only to avoid avmaxte = 0 */
 
   /* time offset between two EPI trains (up to 16 echoes = EPI trains) */
   ksepi_interechotime = ksepi.epitrain.duration + ksepi_echogap + (acq_type == TYPSPIN) * (KS_RFSSP_PRETIME + ksepi.selrfref.pregrad.duration + ksepi.selrfref.grad.duration + ksepi.selrfref.postgrad.duration + KS_RFSSP_POSTTIME);
 
 
   /* maximum TE */
   if (existcv(optr)) {
     if (opautotr) {
       /* TR = minTR, i.e. the current TE is also the maximum TE */
       if (opautote)
         avmaxte = avminte;
       else if (existcv(opte))
         avmaxte = opte;
       else
         avmaxte = avminte;
     } else {
       /* maximum TE dependent on the chosen TR */
       avmaxte = optr - ksepi.seqctrl.ssi_time; /* maximum sequence duration for this TR (implies one slice per TR) */
       avmaxte -= ksepi.spoiler.duration; /* subtract ksepi.spoiler time */
       avmaxte -= ksepi.epitrain.duration - ksepi.epitrain.time2center;
       if (opnecho > 1) {
         avmaxte -= (opnecho - 1) * ksepi_interechotime; /* for multi-echo */
       }
     }
   } else {
     avmaxte = 1s;
   }
 
   if (opnecho == 2) {
     /* for opnecho == 2, the TE2 button appears although we have greyed it out (pite2nub = 0).
        Make avminte2/opte2 contain the actual number */
     avminte2 = avminte + ksepi_interechotime;
     avmaxte2 = avmaxte + ksepi_interechotime;
     opte2 = opte       + ksepi_interechotime;
   }
 
   if (opautote) {
     setpopup(opte, PSD_OFF);
     cvoverride(opte, avminte, PSD_FIX_ON, PSD_EXIST_ON); /* AutoTE: force TE to minimum */
   } else if (existcv(opte)) {
     setpopup(opte, PSD_ON);
     if (opte < avminte)
       return ks_error("TE=%.1f too small. Please increase TE to %.1f", opte / 1000.0, avminte / 1000.0);
     if (opte > avmaxte)
       return ks_error("TE=%.1f too large. Please decrease to %.1f", opte / 1000.0, avmaxte / 1000.0);
   }
 
 
   return SUCCESS;
 
 } /* ksepi_TErange() */

◆ ksepi_eval_inversion()

STATUS ksepi_eval_inversion ( KS_SEQ_COLLECTION * seqcollection )

Wrapper function to KSInversion functions to add single and dual IR support to this sequence

It is important that ksepi_eval_inversion() is called after other sequence modules have been set up and added to the KS_SEQ_COLLECTION struct in my_cveval(). Otherwise the TI and TR timing will be wrong.

Whether IR is on or off is determined by ksinv1_mode, which is set up in KSINV_EVAL()->ksinv_eval(). If it is off, this function will return quietly.

This function calls ksinv_eval_multislice() (KSInversion.e), which takes over the responsibility of TR timing that otherwise is determined in ksepi_eval_tr(). ksinv_eval_multislice() sets seqcollection.evaltrdone = TRUE, which indicates that TR timing has been done. ksepi_eval_tr() checks whether seqcollection.evaltrdone = TRUE to avoid that non-inversion TR timing overrides the TR timing set up in ksinv_eval_multislice().

At the end of this function, TR validation and heat/SAR checks are done.

Parameters

[in,out] seqcollection Pointer to the KS_SEQ_COLLECTION struct holding all sequence modules

Return values

STATUS SUCCESS or FAILURE

                                                               {
   STATUS status;
   int slperpass, npasses;
   int approved_TR = FALSE;
 
   status = KSINV_EVAL(seqcollection, 26, 27, 28, 29); /* args 2-6: integer X corresponds to opuserX CV */
   if (status != SUCCESS) return status;
 
   if (((int) *ksinv1_mode) == KSINV_OFF) {
     /* If no IR1 flag on, return */
     return SUCCESS;
   }
 
   /* interleaved slices in slice gap menu, force 2+ acqs */
   if (opileave)
     npasses = 2;
   else
     npasses = 1;
 
 
   while (approved_TR == FALSE) {
 
     /* Inversion (specific to 2D FSE/EPI type of PSDs). Must be done after all other sequence modules have been set up */
     slperpass = CEIL_DIV((int) exist(opslquant), npasses);
 
     if (KS_3D_SELECTED) {
       status = ks_calc_sliceplan(&ks_slice_plan, exist(opvquant), 1 /* seq 3DMS */);
     } else {
       status = ks_calc_sliceplan(&ks_slice_plan, exist(opslquant), slperpass);
     }
     if (status != SUCCESS) return status;
 
     /* ksinv_eval_multislice() sets seqcollection.evaltrdone = TRUE. This indicates that TR timing has been done.
        ksepi_eval_tr() check whether seqcollection.evaltrdone = TRUE to avoid that non-inversion TR timing overrides the
        intricate TR timing with inversion module(s). At the end of ksinv_eval_multislice(), TR validation and heat/SAR checks are done */
     status = ksinv_eval_multislice(seqcollection, &ks_slice_plan, ksepi_scan_coreslice_nargs, 0, NULL, &ksepi.seqctrl);
     if (status != SUCCESS) return status;
 
     if (existcv(optr) && opflair == OPFLAIR_INTERLEAVED && optr > ksinv_maxtr_t1flair) {
       /* T1-FLAIR */
       if (npasses > exist(opslquant)) {
         return ks_error("%s: T1-FLAIR: TR not met for single slice per TR", __FUNCTION__);
       }
       npasses++; /* increase #passes and call ksinv_eval_multislice() again with a new ks_slice_plan */
     } else {
       /* non-T1-FLAIR, or T1-FLAIR with approved TR value */
       approved_TR = TRUE;
     }
 
   } /* while (approved_TR == FALSE)  */
 
 
   /* Check TR timing and SAR limits */
   status = ksinv_eval_checkTR_SAR(seqcollection, &ks_slice_plan, ksepi_scan_coreslice_nargs, 0, NULL);
   if (status != SUCCESS) return status;
 
 
   return SUCCESS;
 
 } /* ksepi_eval_inversion() */

◆ ksepi_eval_tr()

STATUS ksepi_eval_tr ( KS_SEQ_COLLECTION * seqcollection )

Evaluation of number of slices / TR, set up of slice plan, TR validation and SAR checks

With the current sequence collection (see my_cveval()), and a function pointer to an argument-standardized wrapper function (ksepi_scan_sliceloop_nargs()) to the slice loop function (ksepi_scan_sliceloop(), this function calls GEReq_eval_TR(), where number of slices that can fit within one TR is determined by adding more slices as input argument to the slice loop function. For more details see GEReq_eval_TR().

With the number of slices/TR now known, a standard 2D slice plan is set up using ks_calc_sliceplan() and the duration of the main sequence is increased based on timetoadd_perTR, which was returned by GEReq_eval_TR(). timetoadd_perTR > 0 when optr > avmintr and when heat or SAR restrictions requires avmintr to be larger than the net sum of sequence modules in the slice loop.

This function first checks whether seqcollection.evaltrdone == TRUE. This is e.g. the case for inversion where the TR timing instead is controlled using ksepi_eval_inversion() (calling ksinv_eval_multislice()).

At the end of this function, TR validation and heat/SAR checks are done using GEReq_eval_checkTR_SAR().

Parameters

[in] seqcollection Pointer to the KS_SEQ_COLLECTION struct holding all sequence modules

Return values

STATUS SUCCESS or FAILURE

                                                        {
   int timetoadd_perTR;
   STATUS status;
   int slperpass, min_npasses;
 
   if (seqcollection->evaltrdone == TRUE) {
     /*
      We cannot call GEReq_eval_TR() or GEReq_eval_checkTR_SAR(..., ksepi_scan_sliceloop_nargs, ...) if e.g. the inversion sequence module is used. This is because
      ksinv_scan_sliceloop() is used instead of ksepi_scan_sliceloop(). When ksinv1.params.mode != 0 (i.e. inversion sequence module on), the TR timing and
      heat/SAR limits checks are done in ksinv_eval_multislice(), which is called from ksepi_eval_inversion().
      In the future, other sequence modules may want to take over the responsibility of TR calculations and SAR checks, in which case they need to end their corresponding function
      by setting evaltrdone = TRUE to avoid double processing here */
     return SUCCESS;
   }
 
   /* interleaved slices in slice gap menu, force 2+ acqs */
   if (opileave)
     min_npasses = 2;
   else
     min_npasses = 1;
 
   /* Calculate # slices per TR, # acquisitions and how much spare time we have within the current TR by running the slice loop. */
   status = GEReq_eval_TR(&slperpass, &timetoadd_perTR, min_npasses, seqcollection, ksepi_scan_sliceloop_nargs, 0, NULL);
   if (status != SUCCESS) return status;
 
   /* Calculate the slice plan (ordering) and passes (acqs). ks_slice_plan is passed to GEReq_predownload_store_sliceplan() in predownload() */
   if (KS_3D_SELECTED) {
     ks_calc_sliceplan(&ks_slice_plan, exist(opvquant), 1 /* seq 3DMS */);
   } else {
     ks_calc_sliceplan(&ks_slice_plan, exist(opslquant), slperpass);
   }
 
 
   /* We spread the available timetoadd_perTR evenly, by increasing the .duration of each slice by timetoadd_perTR/ksepi_slperpass */
   ksepi.seqctrl.duration = RUP_GRD(ksepi.seqctrl.duration + CEIL_DIV(timetoadd_perTR, ks_slice_plan.nslices_per_pass));
 
   /* Update SAR values in the UI (error will occur if the sum of sequence durations differs from optr) */
   status = GEReq_eval_checkTR_SAR(seqcollection, ks_slice_plan.nslices_per_pass, ksepi_scan_sliceloop_nargs, 0, NULL);
   if (status != SUCCESS) return status;
 
   /* Fill in the 'tmin' and 'tmin_total'. tmin_total is only like GEs use of the variable when TR = minTR */
   tmin = ksepi.seqctrl.min_duration;
   tmin_total = ksepi.seqctrl.duration;
 
   return SUCCESS;
 
 } /* ksepi_eval_tr() */

◆ ksepi_eval_ssitime()

int ksepi_eval_ssitime ( )

The SSI time for the sequence

Return values

int	SSI time in [us]

                          {
 
   /* SSI time CV:
      Empirical finding on how much SSI time we need to update.
      But, use a longer SSI time when we write out data to file in scan() */
   ksepi_ssi_time = RUP_GRD(IMax(2, 
                           ks_syslimits_hasICEhardware() ? KSEPI_DEFAULT_SSI_TIME_ICEHARDWARE : KSEPI_DEFAULT_SSI_TIME, 
                           _ksepi_ssi_time.minval));
 
   /* Copy SSI CV to seqctrl field used by setssitime() */
   ksepi.seqctrl.ssi_time = RUP_GRD(ksepi_ssi_time);
   ksepi_fleetseq.seqctrl.ssi_time = RUP_GRD(ksepi_ssi_time);
 
   /* SSI time one-sequence-off workaround:
      We set the hardware ssitime in ks_scan_playsequence(), but it acts on the next sequence module, hence
      we aren't doing this correctly when using multiple sequence modules (as KSChemSat etc).
      One option would be to add a short dummy sequence ks_scan_playsequence(), but need to investigate
      if there is a better way. For now, let's assume the the necessary update time is the longest for
      the main sequence (this function), and let the ssi time for all other sequence modules (KSChemSat etc)
      have the same ssi time as the main sequence. */
   kschemsat_ssi_time    = ksepi_ssi_time;
   ksspsat_ssi_time      = ksepi_ssi_time;
   ksinv_ssi_time        = ksepi_ssi_time;
   ksinv_filltr_ssi_time = ksepi_ssi_time;
 
   return ksepi_ssi_time;
 
 } /* ksepi_eval_ssitime() */

◆ ksepi_eval_scantime()

STATUS ksepi_eval_scantime ( )

Set the number of dummy scans for the sequence and calls ksepi_scan_scanloop() to determine

the length of the scan

After setting the number of dummy scans based on the current TR, the ksepi_scan_scanloop() is called to get the scan time. pitscan is the UI variable for the scan clock shown in the top right corner on the MR scanner.

Return values

STATUS SUCCESS or FAILURE

                              {
 
   if (optr > 6s)
     ksepi_dda = 0;
   else if (optr >= 1s)
     ksepi_dda = 1;
   else if (optr > 350ms)
     ksepi_dda = 2;
   else
     ksepi_dda = 4;
 
   if (ksepi_dda > 0)
     ksepi_dda -= ksepi_ghostcorr; /* remove one dummy TR as the ghost corr TR is also acting as one */
 
   pitscan = ksepi_scan_scanloop();
 
   return SUCCESS;
 
 } /* ksepi_eval_scantime() */

◆ ksepi_check()

STATUS ksepi_check ( )

Returns error of various parameter combinations that are not allowed for ksepi

Return values

STATUS SUCCESS or FAILURE

                      {
 
   /* Force the user to select the Echo Planar Imaging button. This error needs to be in cvcheck(), not in
      cvinit()/cveval() to avoid it to trigger also when Echo Planar Imaging has been selected.
      Without opepi = 1, the images won't show up correctly in the GE DB after the 1st volume */
 
   if (!KS_3D_SELECTED && opepi == PSD_OFF) {
     return ks_error("%s: Please first select the 'Echo Planar Imaging' button", ks_psdname);
   }
 
   if (existcv(opte) && existcv(opnex) && opautote == PSD_MINTE && opnex < 1.0) {
     ks_error("%s: TE = MinTE and NEX < 1 is not allowed", __FUNCTION__);
   }
 
   if (ksepi_reflines > ksepi.epitrain.etl) {
     ks_error("%s: ksepi_reflines cannot be larger than echo train length ", __FUNCTION__);
   }
 
   if (existcv(opnshots) && (opasset == ASSET_SCAN) && (opnshots > 1)) {
     return ks_error("%s: ASSET not compatible with multishot", __FUNCTION__);
   }
 
   if (existcv(opnshots) && existcv(opslquant) && existcv(optr) && (!opdiffuse) && (ksepi_multishot_control == KSEPI_MULTISHOT_B0VOLS)) {
     return ks_error("%s: Multishot control can only be 3 for DW-EPI", __FUNCTION__);
   }
 
   if (opasset != 0 && opasset != ASSET_SCAN) {
     return ks_error("%s: ASSET flag must be either 0 (OFF) or 2 (ON)", __FUNCTION__);
   }
 
   if (opdiffuse && oppseq == 2) {
     return ks_error("%s: Select SpinEcho for Diffusion", __FUNCTION__);
   }
 
 
   /* Pixel size in UI */
   piinplaneres = 1;
   ihinplanexres = opfov / ksepi.epitrain.read.res;
   ihinplaneyres = (opfov * opphasefov) / ksepi.epitrain.blipphaser.res;
 
   /* show echo spacing in UI */
   piesp = 1;
   ihesp = ksepi.epitrain.read.grad.duration / 1000.0;
 
   return SUCCESS;
 
 } /* ksepi_check() */

◆ ksepi_predownload_plot()

STATUS ksepi_predownload_plot ( KS_SEQ_COLLECTION * seqcollection )

Plotting of sequence modules and slice timing to PNG/SVG/PDF files

The ks_plot_*** functions used in here will save plots to disk depending on the value of the CV ks_plot_filefmt (see KS_PLOT_FILEFORMATS). E.g. if ks_plot_filefmt = KS_PLOT_OFF, nothing will be written to disk. On the MR scanner, the output will be located in /usr/g/mrraw/plot/<ks_psdname>. In simulation, it will be placed in the current directory (./plot/).

Please see the documentation on how to install the required python version and links. Specifically, there must be a link /usr/local/bin/apython pointing to the Anaconda 2 python binary (v. 2.7).

In addition, the following text files are printed out

<ks_psdname>_objects.txt
<ks_psdname>_seqcollection.txt

Returns: STATUS SUCCESS or FAILURE

                                                                 {
   char tmpstr[1000];
 
   /* System wide (psd independent) option to disable plotting, to e.g. speed up UX on a slow MR show system */
   if (existfile("/usr/g/research/bin/ksdonotplot")) {
     return SUCCESS;
   }
 
 
 #ifdef PSD_HW
   sprintf(tmpstr, "/usr/g/mrraw/%s_objects.txt", ks_psdname);
 #else
   sprintf(tmpstr, "./%s_objects.txt", ks_psdname);
 #endif
   FILE *fp  = fopen(tmpstr, "w");
 
   /* Note: 'fp' can be replaced with 'stdout' or 'stderr' to get these
      values printed out in the WTools window in simulation. However,
      heavy printing may result in that the WTools window closes,
      why we here write to a file ksepi_objects.txt instead */
   ks_print_selrf(ksepi.selrfexc, fp);
   ks_print_selrf(ksepi.selrfref, fp);
   ks_print_selrf(ksepi.selrfref2, fp); /* opdualspinecho = 1, opdiffuse = 1 */
   ks_print_trap(ksepi.diffgrad, fp); /* opdiffuse = 1 */
   ks_print_trap(ksepi.diffgrad2, fp); /* opdualspinecho = 1, opdiffuse = 1 */
   ks_print_epi(ksepi.epitrain, fp);
   ks_print_epi(ksepi.dynreftrain, fp);
   ks_print_trap(ksepi.spoiler, fp);
   fclose(fp);
 
 
   /* ks_plot_host():
   Plot each sequence module as a separate file (PNG/SVG/PDF depending on ks_plot_filefmt (GERequired.e))
   See KS_PLOT_FILEFORMATS in KSFoundation.h for options.
   Note that the phase encoding amplitudes corresponds to the first shot, as set by the call to ksepi_scan_seqstate below */
   ksepi_scan_seqstate(ks_scan_info[0], 0);
 
   KS_PHASEENCODING_PLAN *plans[] = {&ksepi.full_peplan, &ksepi.ref_peplan, &ksepi.peplan};
   int num_plans = sizeof(plans) / sizeof(KS_PHASEENCODING_PLAN *);
   ks_plot_host_seqctrl_manyplans(&ksepi.seqctrl, plans, num_plans);
   ks_plot_host_seqctrl(&ksepi_fleetseq.seqctrl, &ksepi_fleetseq.peplan);
 
   /* Sequence timing plot */
   ks_plot_slicetime_begin();
   ksepi_scan_scanloop();
   ks_plot_slicetime_end();
 
   /* ks_plot_tgt_reset():
   Creates sub directories and clear old files for later use of ksepi_scan_acqloop()->ks_plot_tgt_addframe().
   ks_plot_tgt_addframe() will only write in MgdSim (WTools) to avoid timing issues on the MR scanner. Hence,
   unlike ks_plot_host() and the sequence timing plot, one has to open MgdSim and press RunEntry (and also
   press PlotPulse several times after pressing RunEntry).
   ks_plot_tgt_reset() will create a 'makegif_***.sh' file that should be run in a terminal afterwards
   to create the animiated GIF from the dat files */
   ks_plot_tgt_reset(&ksepi.seqctrl);
 
 
   return SUCCESS;
 
 }  /* ksepi_predownload_plot() */

◆ ksepi_predownload_setrecon()

STATUS ksepi_predownload_setrecon ( )

Last-resort function to override certain recon variables not set up correctly already

For most cases, the GEReq_predownload_*** functions in predownload() in ksepi.e set up the necessary rh*** variables for the reconstruction to work properly. However, if this sequence is customized, certain rh*** variables may need to be changed. Doing this here instead of in predownload() directly separates these changes from the standard behavior.

Return values

STATUS SUCCESS or FAILURE

                                     {
 
   /* GERequired.e uses: rhuser32-25 (VRGF) and rhuser48 (scantime) */
 
   rhuser29 = (float) ksepi_fleet_num_ky; /* store for custom recon to know */
 
   rhuser30 = (float) ksepi_reflines; /* store for custom recon to know */
 
   rhuser31 = (float) ksepi_multishot_control; /* store for custom recon to know */
 
   rhuser47 = (float) opfphases; /* number of imaging volumes (may be less than rhnphases due to cal vols. opfphases does not show up in raw header) */
 
   rhrecon = 961; /* VRE recon using Matlab recon (recon_epi.m). See matlab/deploy/rpmbuild on how to make an RPM */
 
   return SUCCESS;
 
 } /* ksepi_predownload_setrecon() */

◆ ksepi_pg_fleet()

STATUS ksepi_pg_fleet ( int start_time )

The fleet pulse sequence for GRAPPA calibration

This is the fleet pulse sequence in ksepi.e using the sequence objects in KSEPI_FLEET_SEQUENCE with the sequence module name "ksepifleet" (= ksepi_fleet.seqctrl.description)

Return values

STATUS SUCCESS or FAILURE

                                       {
   KS_SEQLOC tmploc = KS_INIT_SEQLOC;
 
   if (ksepi_fleet == FALSE) {
     return SUCCESS;
   }
 
   if (start_time < KS_RFSSP_PRETIME) {
     return ks_error("%s: 1st arg (pos start) must be at least %d us", __FUNCTION__, KS_RFSSP_PRETIME);
   }
 
   /*******************************************************************************************************
    *  RF Excitation
    *******************************************************************************************************/
   tmploc.ampscale = 1.0;
   tmploc.pos = RUP_GRD(start_time + KS_RFSSP_PRETIME);
   tmploc.board = ZGRAD;
 
   /* N.B.: ks_pg_selrf()->ks_pg_rf() detects that ksepi_fleetseq.selrfexc is an excitation pulse
      (ksepi_fleetseq.selrfexc.rf.role = KS_RF_ROLE_EXC) and will also set ksepi_fleetseq.seqctrl.momentstart
      to the absolute position in [us] of the isocenter of the RF excitation pulse */
   if (ks_pg_selrf(&ksepi_fleetseq.selrfexc, tmploc, &ksepi_fleetseq.seqctrl) == FAILURE)
     return FAILURE;
 
   tmploc.pos = ksepi_fleetseq.seqctrl.momentstart;
   tmploc.pos += KS_RFSSP_POSTTIME + ksepi_fleetseq.selrfexc.rf.iso2end + ksepi_fleetseq.selrfexc.grad.ramptime + ksepi_fleetseq.selrfexc.postgrad.duration;
 
   /*******************************************************************************************************
   *  EPI echo time shifting
   *******************************************************************************************************/
   if (ksepi_echotime_shifting == TRUE) {
     tmploc.board = KS_ALL;
     if (ks_pg_wait(&ksepi_fleetseq.pre_delay, tmploc, &ksepi_fleetseq.seqctrl) != SUCCESS) {
       return FAILURE;
     }
     tmploc.pos += GRAD_UPDATE_TIME;
   }
 
   /*******************************************************************************************************
   *  EPI readout including de/rephasers on freq and phase encoding axes (net zero moment on both axes)
   *******************************************************************************************************/
 
   if (ksepi_slicecheck)
     tmploc.board = KS_FREQZ_PHASEY;
   else
     tmploc.board = KS_FREQX_PHASEY;
   tmploc.ampscale = ksepi_readsign;
   if (ks_pg_epi(&ksepi_fleetseq.epitrain, tmploc, &ksepi_fleetseq.seqctrl) == FAILURE) {
     return FAILURE;
   }
   tmploc.pos += ksepi_fleetseq.epitrain.duration; /* end of EPI (incl. x/y rephasers, but not zphaser) */
 
   /*******************************************************************************************************
    *  Gradient spoilers on Y and Z (at the same time)
    *******************************************************************************************************/
   tmploc.ampscale = 1.0;
 
   tmploc.board = YGRAD;
   if (ks_pg_trap(&ksepi_fleetseq.spoiler, tmploc, &ksepi_fleetseq.seqctrl) == FAILURE)
     return FAILURE;
   tmploc.board = ZGRAD;
   if (ks_pg_trap(&ksepi_fleetseq.spoiler, tmploc, &ksepi_fleetseq.seqctrl) == FAILURE)
     return FAILURE;
 
   tmploc.pos += ksepi_fleetseq.spoiler.duration;
 
   /*******************************************************************************************************
   *  EPI echo time shifting
   *******************************************************************************************************/
   if (ksepi_echotime_shifting == TRUE) {
     tmploc.pos += GRAD_UPDATE_TIME;
     tmploc.board = KS_ALL;
     if (ks_pg_wait(&ksepi_fleetseq.post_delay, tmploc, &ksepi.seqctrl) != SUCCESS) {
       return FAILURE;
     }
     tmploc.pos += IMax(2, psd_grd_wait, psd_rf_wait) + GRAD_UPDATE_TIME;
     tmploc.pos += ksepi_echotime_shifting_sumdelay;
   }
 
   /*******************************************************************************************************
    *  Set the minimal sequence duration (ksepi.seqctrl.min_duration) by calling
    *  ks_eval_seqctrl_setminduration()
    *******************************************************************************************************/
 
   /* make sure we are divisible by GRAD_UPDATE_TIME (4us) */
   tmploc.pos = RUP_GRD(tmploc.pos);
 
 #ifdef HOST_TGT
   /* On HOST only: Sequence duration (ksepi_fleetseq.seqctrl.ssi_time must be > 0 and is added to ksepi_fleetseq.seqctrl.min_duration in ks_eval_seqctrl_setminduration() */
   ksepi_fleetseq.seqctrl.ssi_time = ksepi_eval_ssitime();
   ks_eval_seqctrl_setminduration(&ksepi_fleetseq.seqctrl, tmploc.pos); /* tmploc.pos now corresponds to the end of last gradient in the sequence */
 #endif
 
   /*******************************************************************************************************
    * Phase encoding table
    * Need to call this in ksepi_pg_fleet() so it is run both on HOST and TGT. This, since the phase table
    * is dynamically allocated in ks_phaseencoding_generate_epi()->ks_phaseencoding_resize()
    *******************************************************************************************************/
 
   if (ks_phaseencoding_generate_epi(&ksepi_fleetseq.peplan, "Fully sampled EPI volume",
                                       &ksepi_fleetseq.epitrain, 
                                       (ks_enum_epiblipsign) ksepi_blipsign,
                                       KS_PF_EARLY_TE,
                                       ksepi_fleetseq.epitrain.blipphaser.R, 
                                       (ks_enum_sweep_order) KS_SWEEP_ORDER_TOP_DOWN,
                                       ksepi_fleetseq.epitrain.zphaser.numlinestoacq, 
                                       ksepi_caipi) == FAILURE) {
     return FAILURE;
   }
   
   /* set EPI dephasers and blips to the first shot so we get the correct plots in WTools */
   ks_scan_epi_shotcontrol(&ksepi_fleetseq.epitrain, 0, ks_scan_info[0], &ksepi_fleetseq.peplan, 0, 0, 0);
 
   return SUCCESS;
 
 } /* ksepi_pg_fleet() */

◆ ksepi_fleet_scan_seqstate()

STATUS ksepi_fleet_scan_seqstate	(	const SCAN_INFO *	slice_info,
		int	shot
	)

                                                                         {
   float exc_rfphase;
   int exc = 0; /* NEX index. Future use */
 
   /* RF frequency & phase */
   if (ksepi_rfspoiling) {
     exc_rfphase = ks_scan_rf_phase_spoiling(rfspoiling_phase_counter);
     rfspoiling_phase_counter++;
   } else {
     exc_rfphase = 0;
   }
 
   if (slice_info != NULL) {
     ks_scan_rotate(*slice_info);
     ks_scan_rf_on(&ksepi_fleetseq.selrfexc.rf, INSTRALL);
     ks_scan_selrf_setfreqphase(&ksepi_fleetseq.selrfexc, 0, *slice_info, exc_rfphase);
     ks_scan_epi_shotcontrol(&ksepi_fleetseq.epitrain, 0, *slice_info, &ksepi_fleetseq.peplan, shot, exc, exc_rfphase);
   } else {
     ks_scan_rf_off(&ksepi_fleetseq.selrfexc.rf, INSTRALL);
   }
 
   return SUCCESS;
 } /* ksepi_fleet_scan_seqstate() */

◆ ksepi_scan_rf_off()

void ksepi_scan_rf_off ( )

Sets all RF pulse amplitudes to zero

Returns: void

                          {
   ks_scan_rf_off(&ksepi.selrfexc.rf, INSTRALL);
   ks_scan_rf_off(&ksepi.selrfref.rf, INSTRALL);
 
   if (opdiffuse && opdualspinecho) {
     ks_scan_rf_off(&ksepi.selrfref2.rf, INSTRALL);
   }
 }

◆ ksepi_fleet_scan_coreslice()

int ksepi_fleet_scan_coreslice	(	const SCAN_INFO *	slice_pos,
		int	dabslice,
		int	shot
	)

                                                                                    {
   int time = 0;
   float tloc = 0.0;
 
   if (ksepi_fleetseq.seqctrl.duration == 0) {
     return 0;
   }
 
   if (slice_pos != NULL)
     tloc = slice_pos->optloc; /* real slice */
   else
     dabslice = KS_NOTSET; /* shut off data acq if false slice */
 
   ksepi_fleet_scan_seqstate(slice_pos, (rspent == L_SCAN) ? shot  : KS_NOTSET);
   KS_PHASEENCODING_COORD coord = ks_phaseencoding_get(&ksepi_fleetseq.peplan, 0, shot); /* coord to first line of EPI train */
   if (KS_3D_SELECTED) {
     if (ks_scan_info[1].optloc > ks_scan_info[0].optloc)
       dabslice = (opslquant * opvquant - 1) - coord.kz;
     else
       dabslice = coord.kz;
   }
   ks_scan_epi_loadecho(&ksepi_fleetseq.epitrain, 0, 0, dabslice, &ksepi_fleetseq.peplan, shot);
   time += ks_scan_playsequence(&ksepi_fleetseq.seqctrl);
   ks_plot_slicetime(&ksepi_fleetseq.seqctrl, 1, &tloc, ksepi_fleetseq.selrfexc.slthick,
                     slice_pos == NULL ? KS_PLOT_NO_EXCITATION : KS_PLOT_STANDARD);
 
   return time; /* in [us] */
 
 } /* ksepi_fleet_scan_coreslice() */

◆ ksepi_fleet_scan_sliceloop()

int ksepi_fleet_scan_sliceloop	(	int	slperpass,
		int	volindx,
		int	passindx
	)

                                                                          {
   int time = 0;
   int slloc, sltimeinpass, shot;
   SCAN_INFO centerposition = ks_scan_info[0]; /* first slice chosen here, need only rotation stuff */
 
   (void) volindx;
 
   if (KS_3D_SELECTED) {
     int centerslice = opslquant/2;
     /* for future 3D multislab support, let passindx update centerposition */
     centerposition.optloc = (ks_scan_info[centerslice-1].optloc + ks_scan_info[centerslice].optloc)/2.0;
   }
 
   for (sltimeinpass = 0; sltimeinpass < slperpass; sltimeinpass++) {
 
     SCAN_INFO *current_slice = &centerposition;
     if (!KS_3D_SELECTED) {
       /* slice location from slice plan */
       slloc = ks_scan_getsliceloc(&ks_slice_plan, passindx, sltimeinpass);
       current_slice = (slloc != KS_NOTSET) ? &ks_scan_info[slloc] : NULL;
     }
 
     for (shot = -ksepi_fleet_dda; shot < ksepi_fleetseq.peplan.num_shots; shot++) {
 
       if (ksepi_echotime_shifting == TRUE) {
         KS_PHASEENCODING_COORD coord = ks_phaseencoding_get(&ksepi_fleetseq.peplan, 0, shot); /* coord to first line of EPI train */
         const int kyshot = coord.ky % ksepi_fleetseq.peplan.phaser->R;
 
         ks_enum_epiblipsign blipsign = ks_scan_epi_verify_phaseenc_plan(&ksepi_fleetseq.epitrain, &ksepi_fleetseq.peplan, shot);
         int post_delay = 0;
 
         if (blipsign == KS_EPI_POSBLIPS) {
          post_delay = (kyshot <= 0) ? GRAD_UPDATE_TIME : RUP_GRD((int) (ksepi_echotime_shifting_shotdelay * kyshot));
         } else if (blipsign == KS_EPI_NEGBLIPS) {
          post_delay = (kyshot <= 0) ? GRAD_UPDATE_TIME : RUP_GRD((int) (ksepi_echotime_shifting_shotdelay * (ksepi_fleetseq.peplan.phaser->R-1-kyshot)));
         }
 
         ks_scan_wait(&ksepi.pre_delay, ksepi_echotime_shifting_sumdelay - post_delay);
         ks_scan_wait(&ksepi.post_delay, post_delay);
       }
 
       time += ksepi_fleet_scan_coreslice(current_slice, (shot >= 0) ? sltimeinpass : KS_NOTSET, (shot >= 0) ? shot : KS_NOTSET);
 
     }
     ks_plot_slicetime_endofslicegroup(ksepi_fleet_dda > 0 ? "FLEET shots (incl dummies)" : "FLEET shots");
   }
 
   ks_plot_slicetime_endofpass(KS_PLOT_PASS_WAS_CALIBRATION);
 
   return time;
 
 }

◆ ksepi_scan_init()

STATUS ksepi_scan_init ( void )

Common initialization for prescan entry points MPS2 and APS2 as well as the SCAN entry point

Return values

STATUS SUCCESS or FAILURE

                              {
 
   GEReq_initRSP();
 
   /* Here goes code common for APS2, MPS2 and SCAN */
 
   ks_scan_switch_to_sequence(&ksepi.seqctrl);  /* switch to main sequence */
   scopeon(&seqcore); /* Activate scope for core */
   syncon(&seqcore);  /* Activate sync for core */
   setssitime(ksepi.seqctrl.ssi_time / HW_GRAD_UPDATE_TIME);
 
   /* can we make these independent on global rsptrigger and rsprot in orderslice? */
   settriggerarray( (short) ks_slice_plan.nslices_per_pass, rsptrigger);
 
   rfspoiling_phase_counter = 0;
 
   return SUCCESS;
 
 } /* ksepi_scan_init() */

◆ ksepi_scan_prescanloop()

STATUS ksepi_scan_prescanloop	(	int	nloops,
		int	dda
	)

Prescan loop called from both APS2 and MPS2 entry points

Return values

STATUS SUCCESS or FAILURE

                                                    {
   int i, echoindx, sliceindx, shotindx, sltimeinpass;
   int slloc;
 
   /* turn off receivers for all echoes (thanks to slice = KS_NOTSET) */
   for (echoindx = 0; echoindx < opnecho; echoindx++) {
     ks_scan_epi_loadecho(&ksepi.epitrain, echoindx, echoindx, KS_NOTSET, NULL, KS_NOTSET);
   }
   if (ksepi_reflines > 0) {
     /* store phase reference echo as opnecho */
     ks_scan_epi_loadecho(&ksepi.dynreftrain, 0, opnecho, KS_NOTSET, NULL, KS_NOTSET);
   }
 
   /* Diffusion gradients must be off during prescan to get the correct receiver gain */
   if (opdiffuse) {
     ksepi_diffusion_scan_diffamp(&ksepi, KS_NOTSET); /* KS_NOTSET zeroes all diffusion gradient amplitudes */
   }
 
   /* play dummy scans to get into steady state */
   for (i = -dda; i < nloops; i++) {
 
     /* loop over slices */
     for (sltimeinpass = 0; sltimeinpass < ks_slice_plan.nslices_per_pass; sltimeinpass++) {
 
       /* slice location from slice plan */
       slloc = ks_scan_getsliceloc(&ks_slice_plan, 0, sltimeinpass);
 
       /* modify sequence for next playout */
       ksepi_scan_seqstate(ks_scan_info[slloc], KS_NOTSET);
 
       /* data routing control */
       echoindx = 0; /* just to 1st echo for prescan */
       sliceindx = 0;
       shotindx = 0;
       if (i >= 0) {
         ks_scan_epi_loadecho(&ksepi.epitrain, echoindx, echoindx, sliceindx, NULL, shotindx);
       }
 
       ks_scan_playsequence(&ksepi.seqctrl);
 
     } /* for slices */
 
   } /* for nloops */
 
   return SUCCESS;
 
 } /* ksepi_scan_prescanloop() */

◆ ksepi_diffusion_readtensorfile()

STATUS ksepi_diffusion_readtensorfile	(	DIFFSCHEME	diffscheme,
		int	nb0,
		int	ndirs
	)

                                                                                  {
     int i;
     FILE *fp;
     char tmpstr[1000];
     int lineskip = TRUE;
     char matchstr[10];
     int matchlen;
 
 #ifdef PSD_HW
     const char *tensorfile = "/usr/g/bin/tensor.dat";
 #else
     const char *tensorfile = "./tensor.dat";
 #endif
 
     if (nb0 < 0) {
         return ks_error("# T2 (b0) images must be > 0");
     }
 
     if (ndirs < 6 || ndirs > 150) {
         return ks_error("# diff. directions must be in range [6,150]");
     }
 
     /* clear table */
     for (i = 0; i < MAX_DIFSCHEME_LENGTH; i++) {
         diffscheme[XGRAD][i] = diffscheme[YGRAD][i] = diffscheme[ZGRAD][i] = 0.0;
     }
 
 
     /* read from tensor.dat */
 
     if ((fp = fopen(tensorfile, "r" )) == NULL) {
         return ks_error("%s: Could not open file: %s", __FUNCTION__, tensorfile);
     }
 
     /* what to line content look for in the file */
     sprintf(matchstr, "%d", ndirs);
     matchlen = strlen(matchstr);
 
     while (lineskip) {
         fgets(tmpstr, 1000, fp);
         lineskip = strncmp(matchstr, tmpstr, matchlen);
     }
 
     for (i = 0; i < ndirs; i++) {
         if (fgets(tmpstr, 1000, fp) == NULL) {
             ks_error("%s: Error reading file: %s for #dirs = %d, direction %d", __FUNCTION__, tensorfile, ndirs, i);
         }
         sscanf(tmpstr, "%f %f %f", &diffscheme[XGRAD][nb0 + i], &diffscheme[YGRAD][nb0 + i], &diffscheme[ZGRAD][nb0 + i]);
     }
 
     fclose(fp);
 
 
     return SUCCESS;
 }

◆ ksepi_diffusion_getmaxb()

float ksepi_diffusion_getmaxb ( )

                                 {
    float maxb = 0.0;
 #ifdef PSD_HW
     int i;
     /* On the MR scanner, opval should be set to the highest bvalue in the bvalstab list */
     for (i = 0; i < opnumbvals; i++) {
         if (bvalstab[i] > maxb) {
             maxb = bvalstab[i];
         }
     }
 #else
     maxb = opbval;
 #endif    
 
     return maxb;
 }

◆ ksepi_diffusion_set_heat_scaling()

void ksepi_diffusion_set_heat_scaling ( DIFFSCHEME diffscheme )

                                                              {
     int i,N;
     float tmpx = 0, tmpy = 0, tmpz = 0;
     N = opdifnumt2 + ndiffdirs;
     for (i = 0; i < N; i++) {
         tmpx += diffscheme[XGRAD][i] * diffscheme[XGRAD][i];
         tmpy += diffscheme[YGRAD][i] * diffscheme[YGRAD][i];
         tmpz += diffscheme[ZGRAD][i] * diffscheme[ZGRAD][i];
     }
     tmpx = sqrt(tmpx/N);
     tmpy = sqrt(tmpy/N);
     tmpz = sqrt(tmpz/N);
 
     ksepi_diffusion_scaleX_heatcal = tmpx;
     ksepi_diffusion_scaleY_heatcal = tmpy;
     ksepi_diffusion_scaleZ_heatcal = tmpz;
 }

◆ ksepi_diffusion_init_UI()

STATUS ksepi_diffusion_init_UI ( )

                                  {
     int i;
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return SUCCESS;
     }
 
     /* Number of b-values menu (opnumbvals) */
     pinumbnub = 63;
     pinumbval2 = 1;
     pinumbval3 = 2;
     pinumbval4 = 3;
     pinumbval5 = 4;
     pinumbval6 = 5;
 
     cvmax(opbval, 30000);
     cvdef(opbval, 1000);
     opbval = _opbval.defval;
 
     /* b-value table menu */
     pibvalstab = 1; /* show bvalue table */
     if (existcv(opnumbvals) == FALSE) {
         /* until number of b-value has been selected, set up a range of b-values */
         for (i = 0; i < 10; i++)
             bvalstab[i] = 1000 + 500 * i;
     }
 
     avminbvalstab = 10;
     avmaxbvalstab = 20000;
 
     pidifnextab = 1; /* show NEX input in table, but only allow 1 */
     avmindifnextab = 1;
     avmaxdifnextab = 1;
 
     /* Hide number of NEX for T2 menu (opdifnext2) */
     pidifnext2nub = 0;
     avmindifnext2 = 1;
     avmaxdifnext2 = 1;
     cvoverride(opdifnext2, 1, PSD_FIX_ON, PSD_EXIST_ON);
     cvoverride(rhdifnext2, 1, PSD_FIX_ON, PSD_EXIST_ON);
 
 
     /* Number of T2 menu (opdifnumt2) */
     pidifnumt2defval = 1;
     cvdef(opdifnumt2, pidifnumt2defval);
     opdifnumt2 = pidifnumt2defval;
     pidifnumt2nub = 15;
     pidifnumt2val2 = 1;
     pidifnumt2val3 = 2;
     pidifnumt2val4 = 3;
 
     /* Number of diffusion directions menu (opdifnumdirs) */
     pidifnumdirsnub = 15;
     pidifnumdirsdefval = 6;     
     pidifnumdirsval2 = 6;
     pidifnumdirsval3 = 15;
     pidifnumdirsval4 = 25;
 
     /* no synthetic bvalues menu */
     pinumsynbnub = 0;
 
     /* Only allow MinTE (i.e. partial Fourier ky) or MinFullTE */
     pitetype = PSD_LABEL_TE_EFF; /* alt. PSD_LABEL_TE_EFF */
     cvdef(opte, 200ms);
     opte = _opte.defval;
     pite1nub = 6;
     pite1val2 = PSD_MINIMUMTE;
     pite1val3 = PSD_MINFULLTE;
 
     /* Upsample DWI data to nearest power of 2 */
     ksepi_imsize = KS_IMSIZE_POW2;
 
     /* show shots 1-5 */
     pishotval2 = 1;
     pishotval3 = 2;
     pishotval4 = 3;
     pishotval5 = 4;
     pishotval6 = 5;
     cvdef(opnshots, 3);
     opnshots = _opnshots.defval;
 
 
     /* Don't allow multiple acqs for DW-EPI */
     pitrnub = 2; /* Minimum */
     pitrval2 = PSD_MINIMUMTR;
     piisil = PSD_OFF;
 
     /* Optimize TE / super G check box */
 #if EPIC_RELEASE >= 27    
     pimintediflabel = HAVE_PREMIER_GRADIENTS; /* Label indicator: 0 - Optimize TE, 1 - Super G */
     pimintedifvis = HAVE_PREMIER_GRADIENTS; /* Visibility of the "Optimize TE"/"Super G" button : 0 - invisible, 1 - visible */
 #endif
 
 
     /* if ks_gheatfact gets too low, it will trip the gradients during scanning */
     float lowlimit_gheat = (ksepi_diffusion_getmaxb() > 1000.0) ? 0.5 : 0.25;
     if (ks_gheatfact < lowlimit_gheat) {
       cvoverride(ks_gheatfact, lowlimit_gheat, PSD_FIX_OFF, PSD_EXIST_ON);
     }
 
     /* Max diffusion amplitude to work with [G/cm] (based on trial and error) */
     if (HAVE_PREMIER_GRADIENTS) {
         if (opmintedif) { 
 
           if (ks_gheatfact < 0.8) {
             cvoverride(ks_gheatfact, 0.8, PSD_FIX_OFF, PSD_EXIST_ON);
           }
 
           /* 70 mT/m with longer TR */
           _ksepi_diffusion_maxamp.defval = FMin(3, phygrd.xfs, phygrd.yfs, phygrd.zfs);
 
         } else {
           
           /* without increasing min TR for b < 1500, max diff amp seems to be ~50 mT/m (~70%) */
           _ksepi_diffusion_maxamp.defval = 0.70 * FMin(3, phygrd.xfs, phygrd.yfs, phygrd.zfs);
             
         }
     } else {
 
       /* by default, use 85% of physical max to allow for angled slices */
       _ksepi_diffusion_maxamp.defval = 0.85 * FMin(3, phygrd.xfs, phygrd.yfs, phygrd.zfs);
 
     }
 
     ksepi_diffusion_maxamp = _ksepi_diffusion_maxamp.defval;
 
 
     return SUCCESS;
 }

◆ ksepi_diffusion_eval_UI()

STATUS ksepi_diffusion_eval_UI ( )

                                  {
     int i, b, j;
     STATUS status;
     DIFFSCHEME diffscheme_norm1;
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return SUCCESS;
     }
 
 
     /* clear diffusion scheme table */
     for (i = 0; i < MAX_DIFSCHEME_LENGTH; i++) {
         diffscheme[0][i] = diffscheme[1][i] = diffscheme[2][i] = 0.0;
         diffscheme_norm1[0][i] = diffscheme_norm1[1][i] = diffscheme_norm1[2][i] = 0.0;
     }
 
 #ifdef PSD_HW
     {
         float maxb = ksepi_diffusion_getmaxb();
         if (existcv(opnumbvals) && maxb > 0) {
             opbval = maxb;
         }
     }
 #else
     /* In SIM (WTools), we let opbval set bvalstab[] since we are in simulation and can't access bvalstab[] in EvalTool
        If opnumbvals > 1, we make the bvalstab[] a linearly increasing function of opbval with
        bvalstab[opnumbvals-1] = opbval */
     for (i = 0; i < opnumbvals; i++) {
        bvalstab[i] = (i + 1.0) / ((float) opnumbvals) * opbval;
     }
 #endif
 
     /* Diffusion direction menu */
     pidifrecnub = FALSE; /* but on for opdfaxall */
     cvmax(opdifnumdirs, MAX_DIFSCHEME_LENGTH);
 
 
     if (opdfaxall) {
         pidifrecnub = TRUE;
         ndiffdirs = 3;
 
         for (i = 0; i < ndiffdirs; i++) {
             diffscheme[i][opdifnumt2 + i] = 1; /* X, Y, Z */
         }
 
     } else if (opdfax3in1) {
 
         return ks_error("%s: 3in1 is not yet supported", __FUNCTION__);
 
     } else if (opdfaxtetra) {
 
         return ks_error("%s: TETRA is not yet supported", __FUNCTION__);
 
     } else if (optensor) {
 
         if (existcv(opdifnumdirs)) {
             /* we need to rely on number of diffusion directions via 'ndiffdirs' instead of opdifnumdirs (which is
             the value given by the menu) at a time when opdifnumdirs' existflag is set. Later in ksepi_diffusion_predownload_setrecon(),
             if we are doing optensor with multiple b-values, we need to change opdifnumdirs to = opnumbvals * ndiffdirs, and
             at the same time unset the existflag of opdifnumdirs.
             This, since GE does not yet support multi-bvalues for optensor mode, and because the integrated ref scan recon of the
             DTI data unfortunately checks for opdifnumdirs instead of rhnumdifdirs.
             Here, we MUST here check for the existance of opdifnumdirs to avoid recursion when cveval() (and this function) is executed
             after predownload before scanning. */
             ndiffdirs = opdifnumdirs;
         }
 
         /* avoid problems if ndiffdirs = 0 before #directions has been chosen by setting it to 6 */
         if (ndiffdirs == 0)
             ndiffdirs = 6;
 
         status = ksepi_diffusion_readtensorfile(diffscheme, opdifnumt2, ndiffdirs);
         if (status != SUCCESS) return status;
 
     } else {
         ndiffdirs = 1;
 
         /* One diffusion direction (default if none of above matches) */
         /* cvoverride(opdifnumdirs, 1, PSD_FIX_OFF, PSD_EXIST_ON); */
         diffscheme[XGRAD][opdifnumt2] = (opdfaxx != 0);
         diffscheme[YGRAD][opdifnumt2] = (opdfaxy != 0);
         diffscheme[ZGRAD][opdifnumt2] = (opdfaxz != 0);
 
         /* if no opXXX CVs have been set yet (on MR scanner as the PSD loads), default to one direction in Z */
         if (!existcv(opdfaxx) && !existcv(opdfaxy) && !existcv(opdfaxz))
             diffscheme[ZGRAD][opdifnumt2] = 1;
 
     }
 
 
     /* make sure all diffusion directions are normalized */
     for (i = 0; i < ndiffdirs; i++) {
         float dnorm = sqrt(
                           diffscheme[XGRAD][opdifnumt2 + i] * diffscheme[XGRAD][opdifnumt2 + i] +
                           diffscheme[YGRAD][opdifnumt2 + i] * diffscheme[YGRAD][opdifnumt2 + i] +
                           diffscheme[ZGRAD][opdifnumt2 + i] * diffscheme[ZGRAD][opdifnumt2 + i]);
         if (dnorm <= 0.000001) {
             return ks_error("%s: A diffusion direction has zero norm", __FUNCTION__);
         }
         diffscheme_norm1[XGRAD][opdifnumt2 + i] = diffscheme[XGRAD][opdifnumt2 + i] / dnorm;
         diffscheme_norm1[YGRAD][opdifnumt2 + i] = diffscheme[YGRAD][opdifnumt2 + i] / dnorm;
         diffscheme_norm1[ZGRAD][opdifnumt2 + i] = diffscheme[ZGRAD][opdifnumt2 + i] / dnorm;
     }
 
     /* repeat and scale diffusion scheme for multiple b-values */
     for (b = 0; b < opnumbvals; b++) {
         /* The square-root of the b-value ratio is used to scale the diffusion gradients across b-values */
         float gscale = pow( (float) bvalstab[b] / (float) opbval, 0.5);
 
         for (i = 0; i < ndiffdirs; i++) {
             j = i + b * ndiffdirs;
             diffscheme[XGRAD][opdifnumt2 + j] = diffscheme_norm1[XGRAD][opdifnumt2 + i] * gscale;
             diffscheme[YGRAD][opdifnumt2 + j] = diffscheme_norm1[YGRAD][opdifnumt2 + i] * gscale;
             diffscheme[ZGRAD][opdifnumt2 + j] = diffscheme_norm1[ZGRAD][opdifnumt2 + i] * gscale;
         }
     }
 
     /* Save number of volumes total in opfphases based on the length of the diffusion scheme.
        Need to do this here, before we reach predownload() as opfphases is used as an input argument
        to GEReq_predownload_setrecon_epi()->GEReq_predownload_setrecon_voldata(). */
        opfphases = opdifnumt2 + opnumbvals * ndiffdirs;
 
     /* computing root mean sqare averaged diffusion amplitudes for heating calculations
        Note that this is a highly simplified approach, accurate heating estimates can only be computed with pgen_on_host,
        gratHeatMethod = 1 (not supported by KSFoundation at the moment since sequencer instructions are only created on IPG)
        
        Workflow for future implementation of pulsegen on host:
        minseq --> minseqseg --> getCornerpoints --> analyze_gradients calls pulsegen but requires entrypoint calcPulseparams
        calcPulseparams(AVERAGE_POWER) --> sets amplitudes to average
        calcPulseparams(MAXIMUM_POWER) --> sets amplitudes to maximum
     */
     ksepi_diffusion_set_heat_scaling(diffscheme);
 
     /* write diffusion scheme out for debugging */
     {
         FILE *fp;
 #ifdef PSD_HW
         fp = fopen("/usr/g/mrraw/diffusionscheme.txt", "w");
 #else
         fp = fopen("./diffusionscheme.txt", "w");
 #endif
         fprintf(fp, "Max b-value (opbval): %d s/mm^2\n\n", opbval);
         fprintf(fp, "b-values:\n");
         for (i = 0; i < opnumbvals; i++) {
             float gscale = pow( (float) bvalstab[i] / (float) opbval, 0.5);
             fprintf(fp, "%.1f %.2f\n", bvalstab[i], gscale);
         }
         fprintf(fp, "\n");
         for (i = 0; i < opfphases; i++) {
             fprintf(fp, "%f\t%f\t%f\n", diffscheme[XGRAD][i], diffscheme[YGRAD][i], diffscheme[ZGRAD][i]);
         }
         fclose(fp);
     }
 
     return SUCCESS;
 }

◆ SolveCubic()

void SolveCubic	(	double	a,
		double	b,
		double	c,
		double	d,
		int *	nsol,
		double *	x
	)

 {
   double    a1 = b/a, a2 = c/a, a3 = d/a;
   double    Q = (a1*a1 - 3.0*a2)/9.0;
   double    R = (2.0*a1*a1*a1 - 9.0*a1*a2 + 27.0*a3)/54.0;
   double    R2_Q3 = R*R - Q*Q*Q;
   double    theta;
 
   if (R2_Q3 <= 0){
     *nsol = 3;
     theta = acos(R/sqrt(Q*Q*Q));
     x[0] = -2.0 * sqrt(Q) * cos( theta/3.0) - a1/3.0;
     x[1] = -2.0 * sqrt(Q) * cos( (theta+2.0*PI)/3.0) - a1/3.0;
     x[2] = -2.0 * sqrt(Q) * cos( (theta+4.0*PI)/3.0) - a1/3.0;
   } else {
     *nsol = 1;
     x[0] = pow( sqrt(R2_Q3) + fabs(R), 1/3.0);
     x[0] += Q/x[0];
     x[0] *= (R < 0.0) ? 1 : -1;
     x[0] -= a1/3.0;
   }
 
 }

◆ ksepi_diffusion_calcTE()

STATUS ksepi_diffusion_calcTE	(	double *	TE_s,
		int	exciso2end,
		int	crsh1_half180,
		int	half180_crsh2,
		int	crsh3_half180,
		int	half180_crsh4,
		int	readout2echo,
		int	ramptime,
		float	G,
		int	bval_desired,
		int	dualspinechoflag
	)

                                                                                                                                             {
     double exciso2end_s    = 1.0E-6 * RUP_GRD(exciso2end); /* [s] */
     double crsh1_half180_s = 1.0E-6 * RUP_GRD(crsh1_half180); /* [s] */
     double half180_crsh2_s = 1.0E-6 * RUP_GRD(half180_crsh2); /* [s] */
     double crsh3_half180_s = 1.0E-6 * RUP_GRD(crsh3_half180); /* [s] */
     double half180_crsh4_s = 1.0E-6 * RUP_GRD(half180_crsh4); /* [s] */
     double readout2echo_s  = 1.0E-6 * RUP_GRD(readout2echo); /* [s] */
     double ramptime_s      = 1.0E-6 * RUP_GRD(ramptime); /* [s] */
     double fixedtime_s;
     double gam_SI = (2 * PI * 42.58E6); /* [rad/(sT)] */
     double G_SI = G / 100.0; /* [G/cm] -> [T/m] */
     double sol[3];
     int nsol;
     double c0, c1, c2, c3, c0new;
 
     /* all double variables are in SI units (see genbvalcode.m for details on c0-c3 below) */
 
     if (dualspinechoflag) { /* 2x180 */
 
         fixedtime_s = FMax(2, exciso2end_s + crsh1_half180_s, half180_crsh4_s + readout2echo_s) + 2.0 * ramptime_s;
 
         c3 = 1.0 / 1.2E1;
 
         c2 = crsh3_half180_s * (-3.0 / 1.6E1) - exciso2end_s * (1.0 / 1.6E1) - fixedtime_s * (7.0 / 1.6E1) - half180_crsh2_s * (3.0 / 1.6E1) + half180_crsh4_s * (1.0 / 1.6E1) + ramptime_s * (1.0 / 4.0);
 
         c1 = crsh3_half180_s * fixedtime_s * (1.0 / 2.0) + crsh3_half180_s * half180_crsh2_s * (1.0 / 2.0) + exciso2end_s * fixedtime_s * (1.0 / 2.0) + fixedtime_s * half180_crsh2_s * (1.0 / 2.0) - fixedtime_s * half180_crsh4_s * (1.0 / 2.0) -
              exciso2end_s * ramptime_s * (1.0 / 2.0) - fixedtime_s * ramptime_s * (1.0 / 2.0) + half180_crsh4_s * ramptime_s * (1.0 / 2.0) + (crsh3_half180_s * crsh3_half180_s) * (1.0 / 4.0) + (fixedtime_s * fixedtime_s) * (1.0 / 2.0) +
              (half180_crsh2_s * half180_crsh2_s) * (1.0 / 4.0) - (ramptime_s * ramptime_s) * (1.0 / 1.2E1);
 
         c0 = (crsh3_half180_s * crsh3_half180_s) * fixedtime_s * (-1.0 / 2.0) - crsh3_half180_s * (half180_crsh2_s * half180_crsh2_s) * (1.0 / 4.0) - (crsh3_half180_s * crsh3_half180_s) * half180_crsh2_s * (1.0 / 4.0) - exciso2end_s * (fixedtime_s * fixedtime_s) -
              fixedtime_s * (half180_crsh2_s * half180_crsh2_s) * (1.0 / 2.0) + (fixedtime_s * fixedtime_s) * half180_crsh4_s + crsh3_half180_s * (ramptime_s * ramptime_s) * (1.3E1 / 1.2E1) + (crsh3_half180_s * crsh3_half180_s) * ramptime_s * (1.0 / 4.0) -
              exciso2end_s * (ramptime_s * ramptime_s) + fixedtime_s * (ramptime_s * ramptime_s) * (7.0 / 6.0) - (fixedtime_s * fixedtime_s) * ramptime_s + half180_crsh2_s * (ramptime_s * ramptime_s) * (1.3E1 / 1.2E1) + (half180_crsh2_s * half180_crsh2_s) * ramptime_s * (1.0 / 4.0) +
              half180_crsh4_s * (ramptime_s * ramptime_s) - (crsh3_half180_s * crsh3_half180_s * crsh3_half180_s) * (1.0 / 1.2E1) + (fixedtime_s * fixedtime_s * fixedtime_s) * (1.0 / 3.0) - (half180_crsh2_s * half180_crsh2_s * half180_crsh2_s) * (1.0 / 1.2E1) +
              (ramptime_s * ramptime_s * ramptime_s) * (1.0 / 1.5E1) - crsh3_half180_s * fixedtime_s * half180_crsh2_s - crsh3_half180_s * fixedtime_s * ramptime_s + crsh3_half180_s * half180_crsh2_s * ramptime_s * (1.0 / 2.0) + exciso2end_s * fixedtime_s * ramptime_s * 2.0 -
              fixedtime_s * half180_crsh2_s * ramptime_s - fixedtime_s * half180_crsh4_s * ramptime_s * 2.0;
 
     } else { /* 1x180 */
 
         fixedtime_s = FMax(2, exciso2end_s + crsh1_half180_s, half180_crsh2_s + readout2echo_s) + 2.0 * ramptime_s;
 
         c3 = 1.0 / 12.0;
 
         c2 = -(exciso2end_s + fixedtime_s - half180_crsh2_s - ramptime_s) / 4.0;
 
         c1 = exciso2end_s * fixedtime_s - fixedtime_s * half180_crsh2_s - exciso2end_s * ramptime_s + half180_crsh2_s * ramptime_s - ramptime_s * ramptime_s / 12.0;
 
         c0 = (fixedtime_s * fixedtime_s) * half180_crsh2_s - exciso2end_s * (fixedtime_s * fixedtime_s) - exciso2end_s * (ramptime_s * ramptime_s) +
              (7 * fixedtime_s * (ramptime_s * ramptime_s)) / 6 - (fixedtime_s * fixedtime_s) * ramptime_s + half180_crsh2_s * (ramptime_s * ramptime_s) +
              (fixedtime_s * fixedtime_s * fixedtime_s) / 3 - (7 * (ramptime_s * ramptime_s * ramptime_s)) / 15 + 2 * exciso2end_s * fixedtime_s * ramptime_s - 2 * fixedtime_s * half180_crsh2_s * ramptime_s;
 
     }
 
     /* bval = 1.0E-6 * gam_SI * gam_SI * G_SI * G_SI * (c3 * pow(TE_s, 3.0) + c2 * pow(TE_s, 2.0) + c1 * TE_s + c0);  leading 1.0E-6 makes bval in s/mm^2 (e.g. b = 1000)
         where
             double gam_SI = (2 * PI * 42.58E6); [rad/(sT)]
             double G_SI = G [G/cm] / 100.0; [T/m]
 
         b(TE_s) = 1.0E-6 * gam_SI * gam_SI * G_SI * G_SI * (c3 * pow(TE_s, 3.0) + c2 * pow(TE_s, 2.0) + c1 * TE_s + c0);  [s/mm^2]
         desired b-value: bval_desired; [s/mm^2]
         F(TE_s) = b(TE_s) - bval_desired
         Find TE_s that gives F(TE_s) = 0   => TE_s that will yield the correct b-value
         F(TE_s) = 1.0E-6 * gam_SI * gam_SI * G_SI * G_SI * (c3 * pow(TE_s, 3.0) + c2 * pow(TE_s, 2.0) + c1 * TE_s + c0) - bval_desired = 0
         =>
         F(TE_s) = 1.0E-6 * gam_SI * gam_SI * G_SI * G_SI * (c3 * pow(TE_s, 3.0) + c2 * pow(TE_s, 2.0) + c1 * TE_s + (c0 - bval_desired/(1.0E-6 * gam_SI * gam_SI * G_SI * G_SI)))
         => [divide leading factors and make a new c0new = c0 - bval_desired/(1.0E-6 * gam_SI * gam_SI * G_SI * G_SI)
         Fnew(TE_s) = c3 * pow(TE_s, 3.0) + c2 * pow(TE_s, 2.0) + c1 * TE_s + c0new
         Put in c3, c2, c1, c0new into SolveCubic function to get TE_s where F(TE_s) = 0
     */
     c0new = c0 - (double) bval_desired / (1.0E-6 * gam_SI * gam_SI * G_SI * G_SI);
 
     /* Solve cubic function in TE */
     SolveCubic(c3, c2, c1, c0new, &nsol, sol);
 
     if (nsol == 3)
         *TE_s = FMax(3, sol[0], sol[1], sol[2]);
     else
         *TE_s = sol[0];
 
 
     return SUCCESS;
 }

◆ ksepi_diffusion_eval_gradients_TE()

STATUS ksepi_diffusion_eval_gradients_TE ( KSEPI_SEQUENCE * ksepi )

                                                                 {
     double TE_s;
     int exciso2end    = ksepi->selrfexc.rf.iso2end + KS_RFSSP_POSTTIME + ksepi->selrfexc.grad.ramptime + ksepi->selrfexc.postgrad.duration; /* RF excitation isocenter to end of exc rephaser [us] */
     int crsh1_half180 = ksepi->selrfref.pregrad.duration + KS_RFSSP_PRETIME + ksepi->selrfref.grad.ramptime + ksepi->selrfref.rf.start2iso; /* left crusher start to RF isocenter of 1st/only 180 [us] */
     int half180_crsh2 = ksepi->selrfref.rf.iso2end + ksepi->selrfref.grad.ramptime + KS_RFSSP_POSTTIME + ksepi->selrfref.postgrad.duration; /*  RF isocenter to end of right crusher of 1st/only 180 [us] */
     int crsh3_half180 = 0; /* left crusher start to RF isocenter of 2nd 180 (opdualspinecho only) [us] */
     int half180_crsh4 = 0; /* RF isocenter to end of right crusher of 2nd 180 (opdualspinecho only) [us] */
     int fixedtime = 0;
     int bvalue_validated = FALSE;
     int remaining_attempts = 30;
 
     /* Clear both trap objects */
     ks_init_trap(&ksepi->diffgrad);
     ks_init_trap(&ksepi->diffgrad2);
 
     if (ksepi_reflines > 0) {
         exciso2end += ksepi->dynreftrain.duration;
         if (ksepi_slicecheck == FALSE) { /* reflines dephaser may overlap with selrf rephaser unless slicecheck mode */
             exciso2end -= IMin(2, ksepi->dynreftrain.readphaser.duration, ksepi->selrfexc.postgrad.duration);
         }
     }
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return SUCCESS;
     }
 
     /* Diffusion amplitude to start out with [G/cm]. May decrease if b-value very small */
     _ksepi_diffusion_amp.fixedflag = 0;
     ksepi_diffusion_amp = ksepi_diffusion_maxamp;
 
     /* Round the diffusion ramp time to nearest 4 us */
     cvoverride(ksepi_diffusion_ramptime, RUP_GRD(ksepi_diffusion_ramptime), _ksepi_diffusion_ramptime.fixedflag, _ksepi_diffusion_ramptime.existflag);
 
     if (opdualspinecho) {
         crsh3_half180 = ksepi->selrfref2.pregrad.duration + KS_RFSSP_PRETIME + ksepi->selrfref2.grad.ramptime + ksepi->selrfref2.rf.start2iso;
         half180_crsh4 = ksepi->selrfref2.rf.iso2end + ksepi->selrfref2.grad.ramptime + KS_RFSSP_POSTTIME + ksepi->selrfref2.postgrad.duration;
         fixedtime = IMax(2, exciso2end + crsh1_half180, half180_crsh4 + ksepi->pre_delay.duration + ksepi->epitrain.time2center) + 2 * ksepi_diffusion_ramptime;
     } else {
         fixedtime = IMax(2, exciso2end + crsh1_half180, half180_crsh2 + ksepi->pre_delay.duration + ksepi->epitrain.time2center) + 2 * ksepi_diffusion_ramptime;
     }
     fixedtime = RUP_GRD(fixedtime);
 
 
 
     while (bvalue_validated == FALSE) {
 
         if (ksepi_diffusion_calcTE(
             &TE_s, exciso2end /* [us] */, crsh1_half180 /* [us] */, half180_crsh2 /* [us] */, crsh3_half180 /* [us] */,
             half180_crsh4 /* [us] */,  ksepi->epitrain.time2center /* [us] */, ksepi_diffusion_ramptime /* [us] */,
             ksepi_diffusion_amp /* [G/cm] */, opbval /* [s/mm^2] */, opdualspinecho) == FAILURE) {
             return FAILURE;
         }
 
         /* Save the TE found to the CV for later verification. ksepi_diffusion_echotime in [us] */
         cvoverride(ksepi_diffusion_echotime, (TE_s * 1E6), PSD_FIX_OFF, PSD_EXIST_OFF);
         ksepi_diffusion_echotime = RUP_GRD(ksepi_diffusion_echotime);
 
         if (opdualspinecho) {
             /* Set diffusion plateau times based on found TE */
             ksepi->diffgrad.plateautime = RDN_GRD(ksepi_diffusion_echotime / 4 - fixedtime);
             ksepi->diffgrad2.plateautime = RDN_GRD((ksepi_diffusion_echotime / 2 - half180_crsh2 - crsh3_half180 - 4 * ksepi_diffusion_ramptime) / 2);
 
             if ((ksepi->diffgrad.plateautime >= (2 * GRAD_UPDATE_TIME)) && (ksepi->diffgrad2.plateautime >= (2 * GRAD_UPDATE_TIME))) {
                 bvalue_validated = TRUE;
             }
 
             /* Build up the trap object(s) manually, now that we know the plateau time(s) */
             ksepi->diffgrad.amp  = ksepi_diffusion_amp; /* [G/cm] */
             ksepi->diffgrad2.amp = ksepi_diffusion_amp; /* [G/cm] */
             ksepi->diffgrad.ramptime  = ksepi_diffusion_ramptime;
             ksepi->diffgrad2.ramptime = ksepi_diffusion_ramptime;
             strcpy(ksepi->diffgrad.description,  "diffgrad1_4");
             strcpy(ksepi->diffgrad2.description, "diffgrad2_3");
         } else {
             /* Set diffusion plateau times based on found TE */
             ksepi->diffgrad.plateautime = RDN_GRD(ksepi_diffusion_echotime / 2 - fixedtime);
 
             if (ksepi->diffgrad.plateautime >= (2 * GRAD_UPDATE_TIME)) {
                 bvalue_validated = TRUE;
             }
 
             /* Build up the trap object(s) manually, now that we know the plateau time(s) */
             ksepi->diffgrad.amp = ksepi_diffusion_amp; /* [G/cm] */
             ksepi->diffgrad.ramptime = RUP_GRD(ksepi_diffusion_ramptime);
             strcpy(ksepi->diffgrad.description,  "diffgrad");
         }
 
         if (bvalue_validated == FALSE) {
             /* Too low b-value or long ramptimes leading to negative plateau times?
                Reduce diffusion gradient amplitude and try again */
             ksepi_diffusion_amp *= 0.95;
             remaining_attempts--;
             if (remaining_attempts < 0) {
                 return ks_error("%s: TE => negative diffusion gradient plateau time", __FUNCTION__);
             }
         }
     }
 
     /* duration and are are consequences of the fields just set (N.B. all are initialized to zero by ks_init_trap()) */
     ksepi->diffgrad.duration  = ksepi->diffgrad.plateautime  + 2 * ksepi->diffgrad.ramptime;
     ksepi->diffgrad2.duration = ksepi->diffgrad2.plateautime + 2 * ksepi->diffgrad2.ramptime;
     ksepi->diffgrad.area  = ksepi->diffgrad.amp  * (float) (ksepi->diffgrad.plateautime  + ksepi->diffgrad.ramptime);
     ksepi->diffgrad2.area = ksepi->diffgrad2.amp * (float) (ksepi->diffgrad2.plateautime + ksepi->diffgrad2.ramptime);
 
 
     if (ksepi_diffusion_heat_avg == PSD_ON) {
         ksepi->diffgrad.heat_scaling_factor[XGRAD] = ksepi_diffusion_scaleX_heatcal;
         ksepi->diffgrad.heat_scaling_factor[YGRAD] = ksepi_diffusion_scaleY_heatcal;
         ksepi->diffgrad.heat_scaling_factor[ZGRAD] = ksepi_diffusion_scaleZ_heatcal;
         if (opdualspinecho) {
         ksepi->diffgrad2.heat_scaling_factor[XGRAD] = ksepi_diffusion_scaleX_heatcal;
         ksepi->diffgrad2.heat_scaling_factor[YGRAD] = ksepi_diffusion_scaleY_heatcal;
         ksepi->diffgrad2.heat_scaling_factor[ZGRAD] = ksepi_diffusion_scaleZ_heatcal;
         }
     } else {
 
     }
 
 
     return SUCCESS;
 }

◆ ksepi_diffusion_predownload_setrecon()

STATUS ksepi_diffusion_predownload_setrecon ( )

                                               {
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return SUCCESS;
     }
 
 
     /* enforced copying of diffusion related opXXX to rhXXX */
     cvoverride(rhnumbvals, opnumbvals, PSD_FIX_ON, PSD_EXIST_ON);
 
 
     /* mimic GE, but not sure these are needed */
     rhapp_option = opdifproctype; /* does this ever change from 0 ? */
 
     /* opuser 20-25 will be used by GE's DTI feature, but is also good to know for non-tensor
      * for custom off-line DWI recons.
      * rhuser 20,21,22 will be set by recon after reading in tensor.dat
      * 20,21,22 represent the diffusion direction coeffs
      */
     opuser23 = opdifnumt2;
     opuser24 = ndiffdirs;
     rhuser23 = opdifnumt2; /* rhuser 23 and 24 needed by recon to read tensor.dat */
     rhuser24 = ndiffdirs;
     opuser25 = opdualspinecho;
 
     rhnumdifdirs = (ndiffdirs > 1) ? ndiffdirs : 1;
 
     if (optensor) {
 
         rhdptype = 0;
 
         /* multi-bvalue (multi-shell DTI/HARDI) hack for optensor.
         We need to trick GE's diffusion recon to believe we have opdifnumdirs = opnumbvals * ndiffdirs.
         This does not enable the data to be procecced by e.g. GE's FuncTool when opnumbvals > 1, but will put the
         images in the DB for use by external DTI/HARDI software */
         if (opnumbvals > 1 && existcv(opdifnumdirs)) {
             /* MUST make the existflag for opdifnumdirs = 0 here to avoid circular evaluation on HOST
             by calling ksepi_eval_diffusion_UI() and predownload multiple times */
             cvoverride(opdifnumdirs, opnumbvals * ndiffdirs, PSD_FIX_OFF, PSD_EXIST_OFF); /* Don't change PSD_EXIST_OFF */
         }
 
         opuser_usage_tag = DTI_PROC;
         rhuser_usage_tag = DTI_PROC;
 
     } else {
 
 
         opuser_usage_tag = 0;
         rhuser_usage_tag = 0;
 
         /* non-tensor */
         if (opsavedf == 1)
             rhdptype = 1;
         else if (opsavedf == 2)
             rhdptype = 3;
 
     }
 
     return SUCCESS;
 }

◆ ksepi_diffusion_pg()

STATUS ksepi_diffusion_pg	(	KSEPI_SEQUENCE *	ksepi,
		int	TE
	)

                                                          {
     KS_SEQLOC tmploc = KS_INIT_SEQLOC;
     int i;
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return SUCCESS;
     }
 
     /* First diffusion gradient right after the excitation and any reference lines */
     tmploc.ampscale = 1.0;
     tmploc.pos = ksepi->seqctrl.momentstart + ksepi->selrfexc.rf.iso2end + ksepi->selrfexc.grad.ramptime + ksepi->selrfexc.postgrad.duration;
 
     if (ksepi_slicecheck == FALSE) { /* reflines dephaser may overlap with selrf rephaser unless slicecheck mode */
         tmploc.pos -= IMin(2, ksepi->dynreftrain.readphaser.duration, ksepi->selrfexc.postgrad.duration);
     }   
 
     if (ksepi_reflines>0) {
         tmploc.pos += ksepi->dynreftrain.duration;
     }
 
     for (i = XGRAD; i <= ZGRAD; i++) {
         tmploc.board = i;
         if (ks_pg_trap(&ksepi->diffgrad, tmploc, &ksepi->seqctrl) == FAILURE)
             return FAILURE;
     }
 
     /* Selective RF Refocus with left (pregrad.) and right (postgrad.) crushers */
     if (opdualspinecho) {
 
         tmploc.board = ZGRAD;
         tmploc.pos = ksepi->seqctrl.momentstart + RUP_GRD(TE / 4) - ksepi->selrfref.rf.start2iso - ksepi->selrfref.grad.ramptime - ksepi->selrfref.pregrad.duration;
         if (ks_pg_selrf(&ksepi->selrfref, tmploc, &ksepi->seqctrl) == FAILURE)
             return FAILURE;
 
         /* opdualspinecho: Second diffusion gradient after the 1st refocusing pulse */
         tmploc.ampscale = -1.0;
         tmploc.pos += ksepi->selrfref.pregrad.duration + ksepi->selrfref.grad.duration + ksepi->selrfref.postgrad.duration;
         for (i = XGRAD; i <= ZGRAD; i++) {
             tmploc.board = i;
             if (ks_pg_trap(&ksepi->diffgrad2, tmploc, &ksepi->seqctrl) == FAILURE)
                 return FAILURE;
         }
 
         /* opdualspinecho: Third diffusion gradient right after the second */
         tmploc.ampscale = 1.0;
         tmploc.pos += ksepi->diffgrad2.duration;
         for (i = XGRAD; i <= ZGRAD; i++) {
             tmploc.board = i;
             if (ks_pg_trap(&ksepi->diffgrad2, tmploc, &ksepi->seqctrl) == FAILURE)
                 return FAILURE;
         }
 
         tmploc.board = ZGRAD;
         tmploc.pos = ksepi->seqctrl.momentstart + RUP_GRD(TE * 3 / 4) - ksepi->selrfref2.rf.start2iso - ksepi->selrfref2.grad.ramptime - ksepi->selrfref2.pregrad.duration;
         if (ks_pg_selrf(&ksepi->selrfref2, tmploc, &ksepi->seqctrl) == FAILURE)
             return FAILURE;
 
         /* opdualspinecho: Fourth diffusion gradient after the 2nd refocusing pulse */
         tmploc.ampscale = -1.0;
         tmploc.pos += ksepi->selrfref2.pregrad.duration + ksepi->selrfref2.grad.duration + ksepi->selrfref2.postgrad.duration;
         for (i = XGRAD; i <= ZGRAD; i++) {
             tmploc.board = i;
             if (ks_pg_trap(&ksepi->diffgrad, tmploc, &ksepi->seqctrl) == FAILURE)
                 return FAILURE;
         }
 
     } else { /* Stejskal-Tanner diffusion */
 
         tmploc.pos = ksepi->seqctrl.momentstart + TE / 2 - ksepi->selrfref.rf.start2iso - ksepi->selrfref.grad.ramptime - ksepi->selrfref.pregrad.duration;
         if (ks_pg_selrf(&ksepi->selrfref, tmploc, &ksepi->seqctrl) == FAILURE)
             return FAILURE;
 
         /* Second diffusion gradient after the refocusing pulse */
         tmploc.ampscale = 1.0;
         tmploc.pos += ksepi->selrfref.pregrad.duration + ksepi->selrfref.grad.duration + ksepi->selrfref.postgrad.duration;
         for (i = XGRAD; i <= ZGRAD; i++) {
             tmploc.board = i;
             if (ks_pg_trap(&ksepi->diffgrad, tmploc, &ksepi->seqctrl) == FAILURE)
                 return FAILURE;
         }
 
     }
 
     return SUCCESS;
 }

◆ ksepi_diffusion_scan_diffamp()

void ksepi_diffusion_scan_diffamp	(	KSEPI_SEQUENCE *	ksepi,
		int	volindx
	)

                                                                       {
     int i;
 
     if (opdiffuse != KS_EPI_DIFFUSION_ON) {
         return;
     }
 
     /*
        d: ksepi.diffgrad
       d2: ksepi.diffgrad2 (opdualspinecho only)
     #<x>: instance number <x>
 
     opdualspinecho = TRUE (Twice-refocused):
     ========================================
 
              _d#0__                  ____d2#3___
     XGRAD __/      \___             /           \___        ___
                        \___d2#0____/                \__d#3_/
              _d#1__                  ____d2#4___
     YGRAD __/      \___             /           \___        ___
                        \___d2#2____/                \__d#4_/
              _d#2__                  ____d2#5___
     ZGRAD __/      \___             /           \___        ___
                        \___d2#3____/                \__d#5_/
 
 
     opdualspinecho = FALSE (Stejskal-Tanner):
     =========================================
 
              _d#0__     _d#3__
     XGRAD __/      \___/      \___
              _d#1__     _d#4__
     YGRAD __/      \___/      \___
              _d#2__     _d#5__
     ZGRAD __/      \___/      \___
 
     */
 
 
     for (i = XGRAD; i <= ZGRAD; i++) {
         float amp = (volindx >= 0) ? diffscheme[i][volindx] : 0; /* 0 if volindx < 0 */
 
         ks_scan_trap_ampscale_slice(&ksepi->diffgrad, i, 3, 2, amp);
         if (opdualspinecho) {
             ks_scan_trap_ampscale_slice(&ksepi->diffgrad2, i, 3, 2, amp);
         }
     }
 
 
 }

Variable Documentation

◆ seqcollection

KS_SEQ_COLLECTION seqcollection

◆ ksepi_excthickness

float ksepi_excthickness = 0

◆ ksepi_gscalerfexc

float ksepi_gscalerfexc = 0.9 with {0.1, 3.0, 0.9, VIS, "Excitation slice thk scaling (< 1.0 thicker slice)",}

◆ ksepi_slicecheck

int ksepi_slicecheck = 0 with {0, 1, 0, VIS, "move readout to z axis for slice thickness test",}

◆ ksepi_spoilerarea

float ksepi_spoilerarea = 3000.0 with {0.0, 10000.0, 3000.0, VIS, "ksepi ksepi.spoiler gradient area",}

◆ ksepi_rfspoiling

int ksepi_rfspoiling = 1 with {0, 1, 1, VIS, "Enable RF spoiling 1:on 0:off",}

◆ ksepi_fse90

int ksepi_fse90 = 0 with {0, 1, 0, VIS, "Use FSE90 instead of SPSP for non-fatsat",}

◆ ksepi_rf3Dopt

int ksepi_rf3Dopt = 0 with {0, 10, 0, VIS, "Choose optimized SPSP pulse for 3D [0:OFF]",}

◆ ksepi_kissoff_factor

float ksepi_kissoff_factor = 0.04 with {0, 1, 0.04, VIS, "Slice oversampling fraction on each side (3D)",}

◆ ksepi_crusherscale

float ksepi_crusherscale = 1.0 with { -20.0, 20.0, 1.0, VIS, "scaling of crusher gradient area",}

◆ ksepi_gscalerfref

float ksepi_gscalerfref = 0.9 with {0.1, 3.0, 0.9, VIS, "Refocusing slice thk scaling (< 1.0 thicker slice)",}

◆ ksepi_rampsampling

int ksepi_rampsampling = 1 with {0, 1, 1, VIS, "Rampsampling [0:OFF 1:ON]",}

◆ ksepi_readlobegap

int ksepi_readlobegap = 0 with {0, 10ms, 0, VIS, "extra gap between readout lobes [us]",}

◆ ksepi_echogap

int ksepi_echogap = 0 with {0, 100ms, 0, VIS, "extra gap between EPI echoes [us]",}

◆ ksepi_readsign

int ksepi_readsign = 1 with { -1, 1, 1, VIS, "Readout polarity: +1/-1",}

◆ ksepi_readampmax

float ksepi_readampmax = 3.0 with {0.0, 5.0, 3.0, VIS, "Max grad amp for EPI readout lobes",}

◆ ksepi_sr

float ksepi_sr = 0.01 with {0.0, , 0.01, VIS, "EPI SR: amp/ramp [(G/cm) / us]",}

◆ ksepi_esp

int ksepi_esp = 0 with {0, 1000000, 0, VIS, "View-only: Echo spacing in [us]",}

◆ ksepi_blipsign

int ksepi_blipsign = KS_EPI_POSBLIPS with {KS_EPI_NEGBLIPS, KS_EPI_POSBLIPS, KS_EPI_POSBLIPS, VIS, "Blip polarity: +1/-1",}

◆ ksepi_echotime_shifting

int ksepi_echotime_shifting = 1 with {0, 1, 1, VIS, "Enable echo time shifting for multi shot",}

◆ ksepi_kynover

int ksepi_kynover = 24 with {KSEPI_MINHNOVER, 512, 24, VIS, "#extralines for MinTE",}

◆ ksepi_kznover

int ksepi_kznover = 0 with {0, 512, 0, VIS, "#extralines in kz",}

◆ ksepi_ky_R

int ksepi_ky_R = 1 with {1, 512, 1, VIS, "Acceleration in ky",}

◆ ksepi_kz_R

int ksepi_kz_R = 1 with {1, 512, 1, VIS, "Acceleration in kz",}

◆ ksepi_kz_nacslines

int ksepi_kz_nacslines = 16 with {0, 512, 16, VIS, "Number of acs lines in kz",}

◆ ksepi_caipi

int ksepi_caipi = 0 with {0, 512, 0, VIS, "CAIPIRINHA shift (affects 3D epi only. Set 0 for no CAIPI)",}

◆ ksepi_fcy

int ksepi_fcy = 1 with {0, 1, 0, VIS, "Flowcomp Y when opfcomp"}

◆ ksepi_fcz

int ksepi_fcz = 1 with {0, 1, 0, VIS, "Flowcomp Z when opfcomp"}

◆ ksepi_fleet

int ksepi_fleet = 0 with {0, 1, 0, VIS, "FLEET calibration volume [0:OFF 1:ON]",}

◆ ksepi_fleet_flip

float ksepi_fleet_flip = 15.0 with {0.1, 90.0, 15.0, VIS, "FLEET flip angle [deg]",}

◆ ksepi_fleet_dda

int ksepi_fleet_dda = 0 with {0, 200, 0, VIS, "Dummies for FLEET module",}

◆ ksepi_fleet_num_ky

int ksepi_fleet_num_ky = 36 with {1, 512, 36, VIS, "Number of ky encodes for FLEET module",}

◆ ksepi_fleet_num_kz

int ksepi_fleet_num_kz = 24 with {1, 512, 24, VIS, "Number of kz encodes for FLEET module (3D only)",}

◆ ksepi_reflines

int ksepi_reflines = 0 with {0, 96, 0, VIS, "Number of phase reference lines per shot",}

◆ ksepi_swi_returnmode

int ksepi_swi_returnmode = 0 with {0, 7, 0, VIS, "SWI recon 0:Off 1:Acq 2:SWI 4:SWIphase",}

◆ ksepi_pos_start

int ksepi_pos_start = KS_RFSSP_PRETIME with {0, , KS_RFSSP_PRETIME, INVIS, "us from start until the first waveform begins",}

◆ ksepi_ssi_time

int ksepi_ssi_time = KSEPI_DEFAULT_SSI_TIME with {32, , KSEPI_DEFAULT_SSI_TIME, VIS, "time from eos to ssi in intern trig",}

◆ ksepi_dda

int ksepi_dda = 1 with {0, 200, 1, VIS, "Number of dummy scans for steady state",}

◆ ksepi_debug

int ksepi_debug = 1 with {0, 100, 1, VIS, "Write out e.g. plot files (unless scan on HW)"}

◆ ksepi_imsize

int ksepi_imsize = KS_IMSIZE_POW2 with {KS_IMSIZE_NATIVE, KS_IMSIZE_MIN256, KS_IMSIZE_POW2, VIS, "img. upsamp. [0:native 1:pow2 2:min256]"}

◆ ksepi_abort_on_kserror

int ksepi_abort_on_kserror = FALSE with {0, 1, 0, VIS, "Hard program abort on ks_error [0:OFF 1:ON]",}

◆ ksepi_ghostcorr

int ksepi_ghostcorr = 1 with {0, 1, 1, VIS, "Ghost correction [0:OFF 1:ON]",}

◆ ksepi_ref_nsegments

int ksepi_ref_nsegments = 1 with {1, 512, 1, VIS, "Number of kz segments in reference volume",}

◆ ksepi_multishot_control

int ksepi_multishot_control = KSEPI_MULTISHOT_B0VOLS with {KSEPI_MULTISHOT_OFF, KSEPI_MULTISHOT_B0VOLS, KSEPI_MULTISHOT_B0VOLS, VIS, "0:PI 1:All MulShot 2:1stMulShot 3:b0MulShot",}

◆ ksepi_epiqfact

float ksepi_epiqfact = 1.0 with {1.0, 10.0, 1.0, VIS, "Quetness factor for the EPI readout only",}

◆ ksepi

KSEPI_SEQUENCE ksepi = KSEPI_INIT_SEQUENCE

◆ ksepi_fleetseq

KSEPI_FLEET_SEQUENCE ksepi_fleetseq = KSEPI_FLEET_INIT_SEQUENCE

◆ ksepi_interechotime

int ksepi_interechotime = 0

◆ ksepi_echotime_shifting_shotdelay

float ksepi_echotime_shifting_shotdelay = 0

◆ ksepi_echotime_shifting_sumdelay

int ksepi_echotime_shifting_sumdelay = 0

◆ sequence_iopts

int sequence_iopts[]

Initial value:

= {
  PSD_IOPT_ARC, 
  PSD_IOPT_MPH, 
  PSD_IOPT_EDR, 
  PSD_IOPT_ZIP_512, 
  PSD_IOPT_IR_PREP, 
  PSD_IOPT_MILDNOTE, 
  PSD_IOPT_FLOW_COMP, 
  PSD_IOPT_SEQUENTIAL, 
}

◆ rfspoiling_phase_counter

int rfspoiling_phase_counter = 0

◆ ksepi_diffusion_ramptime

int ksepi_diffusion_ramptime = 1500 with {300, 30ms, 1500, VIS, "Ramp times for diffusion gradients", }

◆ ksepi_diffusion_maxamp

float ksepi_diffusion_maxamp = 0.0 with {0.0, 7.0, 3.0, VIS, "Cap for diffusion gradient amplitude", }

◆ ksepi_diffusion_amp

float ksepi_diffusion_amp = 0.0 with {0.0, 7.0, 0.0, VIS, "View-only: Current diffusion gradient amplitude", }

◆ ksepi_diffusion_heat_avg

int ksepi_diffusion_heat_avg = 1 with {0, 1, 1, VIS, "Root mean sqared averaging diffusion amplitudes heat calculations", }

◆ ksepi_diffusion_scaleX_heatcal

float ksepi_diffusion_scaleX_heatcal = 1 with {0, 1, 1, VIS, "View-only: x diffusion gradient amplitude for heating calculations", }

◆ ksepi_diffusion_scaleY_heatcal

float ksepi_diffusion_scaleY_heatcal = 1 with {0, 1, 1, VIS, "View-only: y diffusion gradient amplitude for heating calculations", }

◆ ksepi_diffusion_scaleZ_heatcal

float ksepi_diffusion_scaleZ_heatcal = 1 with {0, 1, 1, VIS, "View-only: z diffusion gradient amplitude for heating calculations", }

◆ ksepi_diffusion_echotime

int ksepi_diffusion_echotime = 0 with {0, , 0, VIS, "View-only: Echo time necessary to meet the desired b-value", }

◆ ksepi_diffusion_2ndcrushfact

float ksepi_diffusion_2ndcrushfact = 2.0 with {0.1, 10.0, 2.0, VIS, "Scale factor for 2nd crusher for opdualspinecho",}

◆ ksepi_diffusion_returnmode

int ksepi_diffusion_returnmode = OFFLINE_DIFFRETURN_ALL with {OFFLINE_DIFFRETURN_ALL, 128, OFFLINE_DIFFRETURN_ALL, VIS, "Diff maps All:0 Acq:1 b0:2 DWI:4 ADC:8 Exp:16 FA:32 cFA:64",}

◆ diffscheme

DIFFSCHEME diffscheme

◆ ndiffdirs

int ndiffdirs = 6

Data Structures

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ KSEPI_MINHNOVER

◆ KSEPI_MAXRBW_NORAMPSAMPLING

◆ KSEPI_DEFAULT_SSI_TIME_ICEHARDWARE

◆ KSEPI_DEFAULT_SSI_TIME

◆ KSEPI_INIT_SEQUENCE1

◆ KSEPI_INIT_SEQUENCE2

◆ KSEPI_INIT_SEQUENCE

◆ KSEPI_FLEET_INIT_SEQUENCE

◆ MAX_DIFSCHEME_LENGTH

Typedef Documentation

◆ DIFFSCHEME

Enumeration Type Documentation

◆ KSEPI_MULTISHOT_MODE

Enums to switch between multishot vs. parallel imaging modes

◆ OFFLINE_DIFFRETURN_MODE

Function Documentation

◆ cvinit()

◆ cveval()

◆ my_cveval()

◆ cvcheck()

◆ predownload()

◆ pulsegen()

◆ mps2()

◆ aps2()

◆ scan()

◆ abstract()

◆ psdname()

◆ ksepi_eval_flowcomp_phase()

◆ ksepi_pg()

The ksepi (main) pulse sequence

◆ ksepi_scan_coreslice()

Plays out one slice in real time during scanning together with other active sequence modules

◆ ksepi_scan_coreslice_nargs()

Wrapper function to ksepi_scan_coreslice() with standardized input arguments

◆ ksepi_scan_sliceloop()

Plays out slperpass slices corresponding to one TR

◆ ksepi_scan_sliceloop_nargs()

Wrapper function to ksepi_scan_sliceloop() with standardized input arguments

◆ ksepi_scan_seqstate()

Sets the current state of all ksepi sequence objects being part of KSEPI_SEQUENCE

◆ ksepi_scan_acqloop()

Plays out all phase encodes for all slices belonging to one pass

◆ ksepi_scan_scanloop()

Plays out all volumes and passes of a single or multi-pass scan

◆ ksepi_init_imagingoptions()

Initial handling of imaging options buttons and top-level CVs at the PSD type-in page

◆ ksepi_init_UI()

Initial setup of user interface (UI) with default values for menus and fields

◆ ksepi_eval_UI()

Gets the current UI and checks for valid inputs

◆ ksepi_eval_setuprf_3dexc()

◆ ksepi_eval_setuprf()

◆ ksepi_eval_setupfleet()

◆ ksepi_eval_setupobjects()

Sets up all sequence objects for the main sequence module (KSEPI_SEQUENCE ksepi)

◆ ksepi_eval_TErange()

Sets the min/max TE based on the durations of the sequence objects in KSEPI_SEQUENCE (ksepi)

◆ ksepi_eval_inversion()

Wrapper function to KSInversion functions to add single and dual IR support to this sequence

◆ ksepi_eval_tr()

Evaluation of number of slices / TR, set up of slice plan, TR validation and SAR checks

◆ ksepi_eval_ssitime()

The SSI time for the sequence

◆ ksepi_eval_scantime()

Set the number of dummy scans for the sequence and calls ksepi_scan_scanloop() to determine

◆ ksepi_check()

Returns error of various parameter combinations that are not allowed for ksepi

◆ ksepi_predownload_plot()

Plotting of sequence modules and slice timing to PNG/SVG/PDF files

◆ ksepi_predownload_setrecon()

Last-resort function to override certain recon variables not set up correctly already

◆ ksepi_pg_fleet()

Plays out `slperpass` slices corresponding to one TR