Hcp_pre_freesurfer potentially fails with GE magnitude/phase field maps (no comlog)

Issues
#1

Hello,
I have troubles to run hcp_pre_freesurfer for my GE sessions. I don’t have any comlog. The command succeed when I write in the batch file _hcp_avgrdcmethod=NONE or _hcp_avgrdcmethod=SiemensFieldMap but not with _hcp_avgrdcmethod=GeneralElectricFieldMap.

It seems that GeneralElectricFieldMap is not working with Phase/Magnitude field maps.

Path to one session:
/gpfs/project/fas/n3/Studies/STIMZO/sessions/06059AE_J00

Command:

qunex_container hcp_pre_freesurfer \
  --sessionids="06038TS_J00,06059AE_J00" \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/STIMZO/sessions" \
  --sessions="/gpfs/project/fas/n3/Studies/STIMZO/processing/batch_clermont_06038TS_06059AE.txt" \
  --overwrite="yes" \
  --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.92.2.sif" \
  --scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=2,mem-per-cpu=8000,partition=pi_anticevic"

Thanks!
Layla

#2

Hi Layla, the support for field map distortion correction on GE scanner is currently rather limited because some issues need to be resolved. I will look into this issue and will let you know as soon as I have more information.

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