As features like e.g. GRAPPA and 3D in ksepi.e are not supported by GE's online recon, raw data (Scan Archives) from ksepi.e needs to be reconstructed in Matlab using the provided matlab_epi directory.

In summer 2024, the old ksepi.e PSD was renamed to ksepi_deprecated.e. This deprecated PSD must be reconstructed using Matlab code in matlab_epi/epi/ as before.

Unless you have an existing ksepi sequence for some time, do not begin working with ksepi_deprecated.e as this comes with no support from Karolinska from now on.

All ks***_deprecated.e PSD will be removed from this repository later in 2024/early 2025.

The new ksepi.e can only be reconstructed using the Matlab code in matlab_epi/epi2/. Note the difference between the (deprecated) epi/ and the (current) epi2/ folder.

Image reconstruction of ksepi.e data (replaced the old ksepi.e PSD in summer 2024)

The image reconstruction handles the following scan modes using ksepi.e

3D T1w EPI
3D SWI EPI
2D Diffusion EPI (with motion correction)
2D fMRI EPI (with motion correction)

Step 1: Getting the Scan Archive on the VRE (GE's recon server)

sdc@mrhost> ssh vre
sdc@vre> cd /data/arc/Closed/Exam\<exno\>/Series\<seno\>
sdc@vre> cp Scan*h5 /usr/g/mrraw/ (shared mount on the MR host)
sdc@vre> exit (exit back to MR host)
sdc@mrhost> cd /usr/g/mrraw/
sdc@mrhost> scp Scan*h5 you@yourcomputer:/some/path/
sdc@mrhost> rm Scan*h5

Karolinska has automatic transfer scripts that moves scan archives to some external server automatically after each scan. Contact us if needed: mrphy.nosp@m.sics.nosp@m.@neur.nosp@m.orad.nosp@m.karol.nosp@m.insk.nosp@m.a.se.

Step 2: Matlab recon of ksepi.e data (2022b or later preferred)

Start Matlab and type: addpath(genpath(~/psd_ksfoundation/matlab_epi))(this adds all subdirs)
recon_ksepi2.m (notice all the flags/options to this recon in epi2/recon_ksepi2_parseinput.m)

Deprecated reconstruction of ksepi_deprecated.e

Most likely this is for those who have used the old ksepi PSD for some time and have their own PSD built from that. This is discouraged for new EPI users, but the recon for this PSD starts with epi/recon_epi.m

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