FreeSurferPipeline

[Fardin Samadi]

Hi team, I'm trying to run freesurfer pipeline, but I have following error:

cat FreeSurferPipeline.sh.e15680

Thu Jun 27 20:08:10 PDT 2024:FreeSurferPipeline.sh: While running '/ifshome/fsamadi/scripts/HCP_Pip/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh --subject=sub_1066_20191221 --subject-dir=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w --t1w-image=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore.nii.gz --t1w-brain=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2w-image=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T2w_acpc_dc_restore.nii.gz':

Thu Jun 27 20:08:10 PDT 2024:FreeSurferPipeline.sh: ERROR: 'recon-all.v6.hires -subjid sub_1066_20191221 -sd /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w -all -i /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -emregmask /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T2w_acpc_dc_restore.nii.gz -T2pial -conf2hires' command failed with return code: 1

===> ERROR: Command returned with nonzero exit code

---------------------------------------------------

         script: FreeSurferPipeline.sh

stopped at line: 573

           call: "${recon_all_cmd[@]}"

  expanded call: recon-all.v6.hires -subjid sub_1066_20191221 -sd /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w -all -i /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -emregmask /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T2w_acpc_dc_restore.nii.gz -T2pial -conf2hires

       hostname: c2025

      exit code: 1

---------------------------------------------------


what is your idea?

[Glasser, Matthew]

I guess you will need to dig a little deeper into the .o file or the recon-all log file to see what the actual error was.

 

Matt.

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[Fardin Samadi]

I have the following in .o file:
........

mri_vol2vol done

#--------------------------------------------

#@# c2hWhiteSurfs lh Thu Jun 27 20:08:09 PDT 2024

cd /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/sub_1066_20191221/mri

mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg rawavg.aseg.presurf.mgz --wm rawavg.wm.mgz --invol rawavg.brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc.rawavg --o ../surf/lh.white.rawavg --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-wmsa --rip-surf ../surf/lh.white.preaparc.rawavg --aparc ../label/lh.aparc.annot

ERROR: reading ../surf/autodet.gw.stats.lh.dat

ERROR:

Linux c2025 3.10.0-1160.99.1.el7.x86_64 #1 SMP Wed Sep 13 14:19:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub_1066_20191221 exited with ERRORS at Thu Jun 27 20:08:10 PDT 2024

For more details, see the log file /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/sub_1066_20191221/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thu Jun 27 20:08:10 PDT 2024:FreeSurferPipeline.sh: While running '/ifshome/fsamadi/scripts/HCP_Pip/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh --subject=sub_1066_20191221 --subject-dir=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w --t1w-image=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore.nii.gz --t1w-brain=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2w-image=/ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T2w_acpc_dc_restore.nii.gz':

Thu Jun 27 20:08:10 PDT 2024:FreeSurferPipeline.sh: ERROR: 'recon-all.v6.hires -subjid sub_1066_20191221 -sd /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w -all -i /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -emregmask /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 /ifs/loni/faculty/farshid/img/shared.data/DABNI/Analysis/sub_1066_20191221/T1w/T2w_acpc_dc_restore.nii.gz -T2pial -conf2hires' command failed with return code: 1

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[Glasser, Matthew]

I’ve never seen that before.  Is it reproducible?

Matt.

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[Fardin Samadi]

I'm resubmitting the job to run again. After receiving the results, I'll review them and hopefully resolve the issue. Just to confirm, I'm using FreeSurfer version 7.1.1. Could this be related to the problem?

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[Glasser, Matthew]

The HCP Pipelines are not compatible with FS 7.X due to surface placement regressions.  We recommend you use FS6.

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