Error with PreFreeSurfer

[Fardin Samadi]

Hi team. I'm try to run this PreFreeSurfer pipeline for my dataset, but I have this error in my log file:
Tue Jun 18 16:23:00 PDT 2024:TopupPreprocessingAll.sh: ERROR: '/usr/local/fsl-6.0.1/bin/imcp' command failed with return code: 1

Tue Jun 18 16:23:00 PDT 2024:TopupPreprocessingAll.sh: ERROR: '/usr/local/fsl-6.0.1/bin/imcp' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: TopupPreprocessingAll.sh
stopped at line: 120
           call: ${FSLDIR}/bin/imcp $PhaseEncodeOne ${WD}/PhaseOne
  expanded call: /usr/local/fsl-6.0.1/bin/imcp /ifs/shared.data/DABNI/Analysis/sub_1066_20191221/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/PhaseOne
       hostname: c2025
      exit code: 1

as I checked, there is no PhaseOne that it is trying to copy. if you have any ideas, I will appreciate them.
Best, Fardin Samadi

[Tim Coalson]

Check the settings for the SpinEchoPhaseEncode* variables in your PreFreeSurfer batch script.  If you don't have spin echo fieldmaps, set them to "NONE" and set the AvgrdcSTRING to something other than TOPUP.

Tim

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