Hcp_pre_freesurfer fails due to field map with excessive phase range

Issues
#1

Hello,
I have troubles to run hcp_pre_freesurfer on my Philips sessions.

The comlog indicates “ERROR: input phase image exceeds allowable phase range. Allowable range is 6.283 radians. Image range is: 71.4188 radians. Aborting.”.

Based on this forum post JISCMail - FSL Archives I used fslmaths to divide the Phase field map per 12. However I couldn’t use fsl_prepare_fieldmap because it’s not working with Philips sessions according to the documentation of fsl_prepare_fieldmap.

Path to one session:
/gpfs/project/fas/n3/Studies/STIMZO/sessions/11071JA_J00

Command:

qunex_container hcp_pre_freesurfer \
  --sessionids="11040SC_J00,11044GS_J00,11050BN_J00,11051SL_J00,11055LF_J00,11062FJ_J00,11063LK_J00,11071JA_J00,11078SB_J00,11080FL_J00" \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/STIMZO/sessions" \
  --sessions="/gpfs/project/fas/n3/Studies/STIMZO/processing/batch_caen.txt" \
  --overwrite="yes" \
  --container="$qunex_container" \
  --scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=2,mem-per-cpu=8000,partition=pi_anticevic"

Output:
error_hcp_pre_freesurfer_11071JA_J00_2022-06-28_15.49.41.035772.log (21.0 KB)

Output after dividing the Phase image per 12:
error_hcp_pre_freesurfer_11071JA_J00_2022-06-28_16.47.05.622578.log (22.3 KB)

Thanks!
Layla

#2

Hi Layla, I will look into this issue shortly and will let you know once it has been resolved.

#3

Layla, to solve the Philips field map distortion correction problem, we need to change the code of the HCP pipelines. For this reason, this solution will take a longer time. I will keep you updated on the progress.

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