Change of repository content

Up until October 2024, the directory structure in the Git master branch has looked like this:

ksgre/ /* Gradient Echo PSD */
ksgre_tutorial/ /* Simple barebone Gradient Echo PSD */
ksfse/ /* Fast Spin Echo PSD */
ksepi/ /* Echo Planar Imaging PSD */
KSFoundation/ /* Folder with KSFoundation libs and RF pulses */
ksmodules/ /* Folder containing *.e files with sequence modules KSChemSat.e, KSInversion.e, KSSpSat.e to be combined with the PSDs */
matlab_epi/ /* Matlab folder with e.g. subfolder epi/ */

As of October 2024, the following name changes have been made (with minimal changes in content):

ksgre/ ==> ksgre_deprecated/
ksfse/ ==> ksfse_deprecated/
ksepi/ ==> ksepi_deprecated/ /* raw data reconstructed with epi/recon_epi.m */
ksmodules/ ==> ksmodules_deprecated/

For those who have worked in one of these PSDs for some time, they may want to merge with ks**_deprecated to make their PSD compatible up to ESE30.2.

But it is recommended to do so only if in hacking/panic mode as these directories will be available only once and a git tag on the master branch in Oct 2024 will mark the latest presence of these PSDs.

Later updates to the master branch will have these folders removed.

Also, Karolinska no longer supports PSD developement using code in these folders. This applies also for the recon code in matlab_epi/epi/, which is used to reconstruct ksepi_deprecated.

The current directory structure

As of October 2024, the previous PSDs have been reworked to be compatible with the new ksmodules/ features, the new phase encoding plans, metadata tags, and the generic scan looping feature.

Current repo:

ksgre/
ksgre_tutorial/ (also reworked)
ksfse/
ksepi/ /* raw data reconstructed with epi2/recon_ksepi2.m */
KSFoundation/ /* Folder with KSFoundation libs and RF pulses */
ksmodules/ /* Folder containing *.e files with sequence modules KSChemSat.e, KSInversion.e, KSSpSat.e to be combined with the PSDs */
matlab_epi/ /* Matlab folder with e.g. subfolders epi/ (old recon) and epi2/ (current recon) */

Note the new spatial/chemical saturation (kssat.e) and inversion modules (ksinversion.h/cc) in ksmodules/.

The new ksmodules/ folder contains the following PSD-independent files:

kschemsat.cc /* Chemical sat */
kschemsat.e /* Chemical sat */
kschemsat.h /* Chemical sat */
ksdesign.cc /* RF design templates, readwave designs etc */
ksdesign.h /* RF design templates, readwave designs etc */
ksdiffusion.cc /* diffusion scheme control (currently used by ksepi.e) */
ksdiffusion.h /* diffusion scheme control (currently used by ksepi.e) */
ksdixon.cc /* Dixon */
ksdixon.h /* Dixon */
ksepg.cc /* extended phase graphs */
ksepg.h /* extended phase graphs */
ksinversion.cc /* inversion control (simple, sliceahead, flairblock) with looping control */
ksinversion.h /* inversion control (simple, sliceahead, flairblock) with looping control */
ksmt.cc /* Magnetization transfer */
ksmt.e /* Magnetization transfer */
ksmt.h /* Magnetization transfer */
ksprop.cc /* Propeller */
ksprop.h /* Propeller */
kssat.e /* Combined chemical, MT, and spatial sat control (uses ksmt.**, ksspsat.**, kschemsat.**) */
ksscan.cc /* generic scan loop control */
ksscan.h /* generic scan loop control */
ksspsat.cc /* Spatial sat */
ksspsat.e /* Spatial sat */
ksspsat.h /* Spatial sat */

New projects should be based on these PSDs and existing long-running projects should ideally be started over from one of these PSDs as a base when time permits.

For the PSD transition to be smooth, please read the other HowTos.

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