Hcp_pre_freesurfer fails due to field map with excessive phase range

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:


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" \

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)


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

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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