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poldracklab / tacc-openneuro

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ds001555-fmriprep (minimal mode): "mritotal: Command not found." #76

Closed jbwexler closed 4 weeks ago

jbwexler commented 9 months ago

For 2/3 subjects from a sample run of ds001555:

    mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.158285/src.mnc transforms/talairach.auto.xfm
    mritotal: Command not found.
    ERROR: mritotal failed, see transforms/talairach.log

transforms/talairach.log: /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds001555-fmriprep/sourcedata/freesurfer/sub-001/mri /opt/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach 7.3.2 Linux c210-012.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Fri Aug 25 02:18:23 UTC 2023 tmpdir is transforms/tmp.talairach.173159 /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds001555-fmriprep/sourcedata/freesurfer/sub-001/mri mri_convert orig_nu.mgz transforms/tmp.talairach.173159/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.173159/src.mnc reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.173159/src.mnc...

effigies commented 9 months ago

Recently got a fix in. Will update the docker image this week.