[RESOLVED] Hcp_fmri_volume error with legacy data when no scout is provided


When running hcp_fmri_volume on legacy data it fails with the error: ERROR: Intended fMRI Reference does not exist (/gpfs/loomis/pi/n3/Studies/Psi.Med/sessions/5107_M1/hcp/5107_M1/BOLD_1/Scout_gdc


qunex hcp_fmri_volume \
 --sessions="/gpfs/project/fas/n3/Studies/Psi.Med/processing/5107_M1_batch_test.txt" \
 --sessionsfolder="/gpfs/project/fas/n3/Studies/Psi.Med/sessions/" \
 --parsessions="1" \
 --parelements="2" \
 --overwrite="yes" \
 --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-latest.sif" \



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Flora, hi!

I reviewed the error logs in your study and found the underlying issue. Let me explain. The important parts are the following settings in your batch file:

  • _hcp_bold_slicetimerparams : odd
  • _hcp_bold_movref : first

The primary reason for the failure is the first setting. Namely, when specifying parameters that are to be passed on to fsl slicetimer using hcp_bold_slicetimerparams, the parameters need to be entered in the exact same way as in a call to slicetimer. What happened in this case was:

(i) With bold 1 the processing went all the way to slice timing correction, but when slicetimer was run, it did not recognize odd as a valid argument and the execution stopped without bold 1 being fully processed.
(ii) Because you have specified to use bold 1 as movement correction reference for all other bold images (using hcp_bold_moveref), the processing of all other bold images failed when the relevant bold 1 reference image was not found. This occurred before the slice timing correction step and gave the error you reported.

The solution to your issue then is to specify:

_hcp_bold_slicetimerparams : --odd

We’ll edit the inline help to make the use of slicetimer parameters clearer.

All the best,