ds004007-fmriprep: "The fsaverage link probably points to an older freesurfer version"

jbwexler commented 2 years ago

I've come across this error in a few different datasets recently. As far as I can tell, I've never run these datasets with an earlier version of fmriprep, nor have I copied in any fsaverage files.

/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004007-fmriprep/sourcedata/free surfer/sub-20

mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brain mask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray -- in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-20

setting seed for random number genererator to 1234

7.2.0 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcort gray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-c tx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-20 sysname Linux hostname c183-042.frontera.tacc.utexas.edu machine x86_64 user jbwexler whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1753772 mm^3 (det: 1.110809 ) Computing euler number orig.nofix lheno = -32, rheno = -22 orig.nofix lhholes = 17, rhholes = 12 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab MRIcopyHeader(): source has ctab

Reporting on 45 segmentations Using PrintSegStat mri_segstats done /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004007-fmriprep/sourcedata/freesurfer/sub-20/label

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@# BA_exvivo Labels lh Wed Nov 9 13:25:48 UTC 2022

ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version

Linux c183-042.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-20 exited with ERRORS at Wed Nov 9 13:25:48 UTC 2022

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

jbwexler commented 2 years ago

@effigies @mgxd

effigies commented 2 years ago

This is weird:

$ ls /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004007-fmriprep/sourcedata/freesurfer/fsaverage/label/ | grep exvivo
lh.BA3b_exvivo.label
lh.BA3b_exvivo.thresh.label
lh.BA44_exvivo.label
lh.BA44_exvivo.thresh.label
lh.BA45_exvivo.label
lh.BA45_exvivo.thresh.label
lh.BA4a_exvivo.label
lh.BA4a_exvivo.thresh.label
lh.BA4p_exvivo.label
lh.BA4p_exvivo.thresh.label
lh.BA6_exvivo.label
lh.BA6_exvivo.thresh.label
lh.entorhinal_exvivo.label
lh.entorhinal_exvivo.thresh.label
lh.MT_exvivo.label
lh.MT_exvivo.thresh.label
lh.perirhinal_exvivo.label
lh.perirhinal_exvivo.thresh.label
lh.V1_exvivo.label
lh.V1_exvivo.thresh.label
lh.V2_exvivo.label
lh.V2_exvivo.thresh.label
rh.BA1_exvivo.label
rh.BA1_exvivo.thresh.label
rh.BA2_exvivo.label
rh.BA2_exvivo.thresh.label
rh.BA3a_exvivo.label
rh.BA3a_exvivo.thresh.label
rh.BA3b_exvivo.label
rh.BA3b_exvivo.thresh.label
rh.BA44_exvivo.label
rh.BA44_exvivo.thresh.label
rh.BA45_exvivo.label
rh.BA45_exvivo.thresh.label
rh.BA4a_exvivo.label
rh.BA4a_exvivo.thresh.label
rh.BA4p_exvivo.label
rh.BA4p_exvivo.thresh.label
rh.BA6_exvivo.label
rh.BA6_exvivo.thresh.label
rh.entorhinal_exvivo.label
rh.entorhinal_exvivo.thresh.label
rh.MT_exvivo.label
rh.MT_exvivo.thresh.label
rh.perirhinal_exvivo.label
rh.perirhinal_exvivo.thresh.label
rh.V1_exvivo.label
rh.V1_exvivo.thresh.label
rh.V2_exvivo.label
rh.V2_exvivo.thresh.label

BA1 and BA2 are missing for lh but not rh. They do exist in the image:

$ singularity exec /scratch1/03201/jbwexler/openneuro_derivatives/containers/images/bids/bids-fmriprep--22.0.2.sing ls /opt/freesurfer/subjects/fsaverage/label/ | grep exvivo
lh.BA1_exvivo.label
lh.BA1_exvivo.thresh.label
lh.BA2_exvivo.label
lh.BA2_exvivo.thresh.label
lh.BA3a_exvivo.label
lh.BA3a_exvivo.thresh.label
lh.BA3b_exvivo.label
lh.BA3b_exvivo.thresh.label
lh.BA44_exvivo.label
lh.BA44_exvivo.thresh.label
lh.BA45_exvivo.label
lh.BA45_exvivo.thresh.label
lh.BA4a_exvivo.label
lh.BA4a_exvivo.thresh.label
lh.BA4p_exvivo.label
lh.BA4p_exvivo.thresh.label
lh.BA6_exvivo.label
lh.BA6_exvivo.thresh.label
lh.MT_exvivo.label
lh.MT_exvivo.thresh.label
lh.V1_exvivo.label
lh.V1_exvivo.thresh.label
lh.V2_exvivo.label
lh.V2_exvivo.thresh.label
lh.entorhinal_exvivo.label
lh.entorhinal_exvivo.thresh.label
lh.perirhinal_exvivo.label
lh.perirhinal_exvivo.thresh.label
rh.BA1_exvivo.label
rh.BA1_exvivo.thresh.label
rh.BA2_exvivo.label
rh.BA2_exvivo.thresh.label
rh.BA3a_exvivo.label
rh.BA3a_exvivo.thresh.label
rh.BA3b_exvivo.label
rh.BA3b_exvivo.thresh.label
rh.BA44_exvivo.label
rh.BA44_exvivo.thresh.label
rh.BA45_exvivo.label
rh.BA45_exvivo.thresh.label
rh.BA4a_exvivo.label
rh.BA4a_exvivo.thresh.label
rh.BA4p_exvivo.label
rh.BA4p_exvivo.thresh.label
rh.BA6_exvivo.label
rh.BA6_exvivo.thresh.label
rh.MT_exvivo.label
rh.MT_exvivo.thresh.label
rh.V1_exvivo.label
rh.V1_exvivo.thresh.label
rh.V2_exvivo.label
rh.V2_exvivo.thresh.label
rh.entorhinal_exvivo.label
rh.entorhinal_exvivo.thresh.label
rh.perirhinal_exvivo.label
rh.perirhinal_exvivo.thresh.label

So it seems that there is an issue with the copy or the datalad save on these files.

WangYunHong98 commented 8 months ago

I got the same error as you, did you solve it please? @jbwexler

jbwexler commented 8 months ago

Hi Wang, I never solved this issue per se but I haven't encountered it in a while. Are you also missing lh.BA1 and lh.BA2?

WangYunHong98 commented 8 months ago

Hi @jbwexler , I am missing only lh.BA1. One solution I used is that I specified --fs-subjects-dir /output/freesurfer.

poldracklab / tacc-openneuro

ds004007-fmriprep: "The fsaverage link probably points to an older freesurfer version" #45

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@# BA_exvivo Labels lh Wed Nov 9 13:25:48 UTC 2022

ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version