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ds003669-fmriprep: "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***" #82

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jbwexler opened this issue Jun 3, 2024 · 1 comment
Open

ds003669-fmriprep: "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***" #82

jbwexler opened this issue Jun 3, 2024 · 1 comment
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fmriprep Affects fMRIPrep

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@jbwexler
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jbwexler commented Jun 3, 2024

About half the subjects had similar errors:

    data/freesurfer/sub-MP02312/mri/orig/001.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz


     mri_info /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz

    rawavg.mgz ========================================
    Volume information for /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz
              type: MGH
        dimensions: 176 x 256 x 256
       voxel sizes: 1.000000, 1.000000, 1.000000
              type: FLOAT (3)
               fov: 256.000
               dof: 1
            xstart: -88.0, xend: 88.0
            ystart: -128.0, yend: 128.0
            zstart: -128.0, zend: 128.0
                TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
           nframes: 1
           PhEncDir: UNKNOWN
           FieldStrength: 0.000000
    ras xform present
        xform info: x_r =   1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.5000
                  : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =    17.0225
                  : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =   -34.8087

    talairach xfm :
    Orientation   : RAS
    Primary Slice Direction: axial

    voxel to ras transform:
                    1.0000   0.0000   0.0000   -87.5000
                    0.0000   1.0000   0.0000  -110.9775
                    0.0000   0.0000   1.0000  -162.8087
                    0.0000   0.0000   0.0000     1.0000

    voxel-to-ras determinant 1

    ras to voxel transform:
                    1.0000   0.0000   0.0000    87.5000
                    0.0000   1.0000   0.0000   110.9775
                    0.0000   0.0000   1.0000   162.8087
                    0.0000   0.0000   0.0000     1.0000
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312

     mri_convert /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz --conform

    mri_convert /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz --conform
    reading from /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz...
    TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    i_ras = (1, 0, 0)
    j_ras = (0, 1, 0)
    k_ras = (0, 0, 1)
    changing data type from float to uchar (noscale = 0)...
    MRIchangeType: Building histogram 0 4095 1000, flo=0, fhi=0.999, dest_type=0
    Reslicing using trilinear interpolation
    writing to /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz...

     mri_add_xform_to_header -c /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach.xfm /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz

    INFO: extension is mgz

     mri_info /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz

    orig.mgz ========================================
    Volume information for /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz
              type: MGH
        dimensions: 256 x 256 x 256
       voxel sizes: 1.000000, 1.000000, 1.000000
              type: UCHAR (0)
               fov: 256.000
               dof: 1
            xstart: -128.0, xend: 128.0
            ystart: -128.0, yend: 128.0
            zstart: -128.0, zend: 128.0
                TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
           nframes: 1
           PhEncDir: UNKNOWN
           FieldStrength: 0.000000
    ras xform present
        xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.5000
                  : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    17.0225
                  : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =   -34.8087

    talairach xfm : /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach.xfm
    Orientation   : LIA
    Primary Slice Direction: coronal

    voxel to ras transform:
                   -1.0000   0.0000   0.0000   128.5000
                    0.0000   0.0000   1.0000  -110.9775
                    0.0000  -1.0000   0.0000    93.1913
                    0.0000   0.0000   0.0000     1.0000

    voxel-to-ras determinant -1

    ras to voxel transform:
                   -1.0000  -0.0000  -0.0000   128.5000
                   -0.0000  -0.0000  -1.0000    93.1913
                   -0.0000   1.0000  -0.0000   110.9775
                   -0.0000  -0.0000  -0.0000     1.0000
    #--------------------------------------------
    #@# Talairach Fri May  3 17:33:20 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    /opt/freesurfer/bin/mri_nu_correct.mni
    --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
    nIters 1
    mri_nu_correct.mni 7.3.2
    Linux c110-191.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 May  3 17:33:20 UTC 2024
    tmpdir is ./tmp.mri_nu_correct.mni.279572
    cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.279572/nu0.mgz --dtype uchar
    AntsN4BiasFieldCorrectionFs done
    mri_convert ./tmp.mri_nu_correct.mni.279572/nu0.mgz orig_nu.mgz --like orig.mgz --conform
    mri_convert ./tmp.mri_nu_correct.mni.279572/nu0.mgz orig_nu.mgz --like orig.mgz --conform
    reading from ./tmp.mri_nu_correct.mni.279572/nu0.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)
    INFO: transform src into the like-volume: orig.mgz
    writing to orig_nu.mgz...


    Fri May  3 17:36:41 UTC 2024
    mri_nu_correct.mni done

     talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

    talairach_avi log file is transforms/talairach_avi.log...
    mv -f /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
    Started at Fri May 3 17:36:41 UTC 2024
    Ended   at Fri May  3 17:37:01 UTC 2024
    talairach_avi done

     cp transforms/talairach.auto.xfm transforms/talairach.xfm

    lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
    7.3.2

    --src: orig.mgz src image (geometry).
    --trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
    --inmni: transforms/talairach.xfm input MNI/XFM transform.
    --outlta: transforms/talairach.xfm.lta output LTA.
    --s: fsaverage subject name
    --ltavox2vox: output LTA as VOX_TO_VOX transform.
     LTA read, type : 1
     0.99830   0.05431   0.01687   0.19576;
    -0.29411   3.32086  -1.84695  -63.01923;
     0.14737  -1.86987   2.62712   39.53989;
     0.00000   0.00000   0.00000   1.00000;
    setting subject to fsaverage
    Writing  LTA to file transforms/talairach.xfm.lta...
    lta_convert successful.
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    #--------------------------------------------
    #@# Talairach Failure Detection Fri May  3 17:37:03 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri

     talairach_afd -T 0.005 -xfm transforms/talairach.xfm

    ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

    Manual Talairach alignment may be necessary, or
    include the -notal-check flag to skip this test,
    making sure the -notal-check flag follows -all
    or -autorecon1 in the command string.
    See:

    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

    INFO: Retrying Talairach align using 3T-based atlas...

    #--------------------------------------------
    #@# Talairach Fri May  3 17:37:03 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux c110-191.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 May 3 17:37:03 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.882
cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.882/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.882/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.882/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.882/nu0.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)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...

    Fri May  3 17:40:23 UTC 2024
    mri_nu_correct.mni done

     talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig

    talairach_avi log file is transforms/talairach_avi.log...
    mv -f /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt
    Started at Fri May 3 17:40:24 UTC 2024
    Ended   at Fri May  3 17:40:43 UTC 2024
    talairach_avi done

     cp transforms/talairach.auto.xfm transforms/talairach.xfm

    lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
    7.3.2

    --src: orig.mgz src image (geometry).
    --trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
    --inmni: transforms/talairach.xfm input MNI/XFM transform.
    --outlta: transforms/talairach.xfm.lta output LTA.
    --s: fsaverage subject name
    --ltavox2vox: output LTA as VOX_TO_VOX transform.
     LTA read, type : 1
     0.98975   0.06058   0.03071  -0.51796;
    -0.09829   1.17042   0.16216  -14.36108;
    -0.01288  -0.18079   1.09896   3.51234;
     0.00000   0.00000   0.00000   1.00000;
    setting subject to fsaverage
    Writing  LTA to file transforms/talairach.xfm.lta...
    lta_convert successful.
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    #--------------------------------------------
    #@# Talairach Failure Detection Fri May  3 17:40:45 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri

     talairach_afd -T 0.005 -xfm transforms/talairach.xfm

    talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7153, pval=0.4932 >= threshold=0.0050)

     awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach_avi.log


     tal_QC_AZS /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach_avi.log

    TalAviQA: 0.89852
    z-score: -18
    WARNING: Talairach QA check failed!
    z-score of -18 is <= threshold of -9


    Manual Talairach alignment may be necessary, or
    include the -notal-check flag to skip this test,
    making sure the -notal-check flag follows -all
    or -autorecon1 in the command string.
    See:

    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

    INFO: Trying MINC mritotal to perform Talairach align...

    #--------------------------------------------
    #@# Talairach Fri May  3 17:40:45 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    /opt/freesurfer/bin/mri_nu_correct.mni
    --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
    nIters 1
    mri_nu_correct.mni 7.3.2
    Linux c110-191.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 May  3 17:40:45 UTC 2024
    tmpdir is ./tmp.mri_nu_correct.mni.8161
    cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
    AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.8161/nu0.mgz --dtype uchar
    AntsN4BiasFieldCorrectionFs done
    mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
    mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
    reading from ./tmp.mri_nu_correct.mni.8161/nu0.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)
    INFO: transform src into the like-volume: orig.mgz
    writing to orig_nu.mgz...



     tal_QC_AZS /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmripre

p/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach_avi.log

    TalAviQA: 0.89852
    z-score: -18
    WARNING: Talairach QA check failed!
    z-score of -18 is <= threshold of -9


    Manual Talairach alignment may be necessary, or
    include the -notal-check flag to skip this test,
    making sure the -notal-check flag follows -all
    or -autorecon1 in the command string.
    See:

    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

    INFO: Trying MINC mritotal to perform Talairach align...

    #--------------------------------------------
    #@# Talairach Fri May  3 17:40:45 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000

--distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri May 3 17:40:45 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.8161
cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourced
ata/freesurfer/sub-MP02312/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.8161/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.8161/nu0.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)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...

    tmpdir is ./tmp.mri_nu_correct.mni.8161

args =
big_ventricles =
brainstem =
directive = autorecon1
environ = {}
expert =
flags =
hemi =
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires =
mprage =
mri_aparc2aseg =
mri_ca_label =
mri_ca_normalize =
mri_ca_register =
mri_edit_wm_with_aseg =
mri_em_register =
mri_fill =
mri_mask =
mri_normalize =
mri_pretess =
mri_remove_neck =
mri_segment =
mri_segstats =
mri_tessellate =
mri_watershed =
mris_anatomical_stats =
mris_ca_label =
mris_fix_topology =
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 7
parallel =
steps =
subject_id = recon_all
subjects_dir =
talairach =
use_FLAIR =
use_T2 =
xopts =

Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
Node: fmriprep_23_2_wf.sub_MP02312_wf.anat_fit_wf.surface_recon_wf.autorecon1
Working directory: /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_MP02312_wf/anat
_fit_wf/surface_recon_wf/autorecon1

Node inputs:

FLAIR_file =
T1_files =
T2_file =
args =
big_ventricles =
brainstem =
directive = autorecon1
environ = {}
expert =
flags =
hemi =
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires =
mprage =
mri_aparc2aseg =
mri_ca_label =
mri_ca_normalize =
mri_ca_register =
mri_edit_wm_with_aseg =
mri_em_register =
mri_fill =
mri_mask =
mri_normalize =
mri_pretess =
mri_remove_neck =
mri_segment =
mri_segstats =
mri_tessellate =
mri_watershed =
mris_anatomical_stats =
mris_ca_label =
mris_fix_topology =
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 7
parallel =
steps =
subject_id = recon_all
subjects_dir =
talairach =
use_FLAIR =
use_T2 =
xopts =

Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771
, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1.

Cmdline:
recon-all -autorecon1 -i /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_M
P02312_wf/anat_fit_wf/anat_validate/sub-MP02312_T1w_noise_corrected_ras_valid.nii -noskullstrip -noT2pia
l -noFLAIRpial -openmp 7 -subjid sub-MP02312 -sd /scratch1/03201/jbwexler/openneuro_derivatives/derivati
ves/fmriprep/ds003669-fmriprep/sourcedata/freesurfer
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 7
parallel =
steps =
subject_id = recon_all
subjects_dir =
talairach =
use_FLAIR =
use_T2 =
xopts =

Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771
, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1.

Cmdline:
recon-all -autorecon1 -i /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_M
P02312_wf/anat_fit_wf/anat_validate/sub-MP02312_T1w_noise_corrected_ras_valid.nii -noskullstrip -noT2pia
l -noFLAIRpial -openmp 7 -subjid sub-MP02312 -sd /scratch1/03201/jbwexler/openneuro_derivatives/derivati
ves/fmriprep/ds003669-fmriprep/sourcedata/freesurfer
Stdout:
fs-check-version --s sub-MP02312 --o /tmp/tmp.v8ywxo
Fri May 3 17:33:06 UTC 2024

    setenv SUBJECTS_DIR /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669

-fmriprep/sourcedata/freesurfer
cd /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_MP02312_wf/anat_fit_wf/
surface_recon_wf/autorecon1
/opt/freesurfer/bin/fs-check-version --s sub-MP02312 --o /tmp/tmp.v8ywxo
-rwxrwxr-x 1 nobody nogroup 18565 Aug 4 2022 /opt/freesurfer/bin/fs-check-version

    freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
    $Id$
    Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT

C 2023 x86_64 x86_64 x86_64 GNU/Linux
pid 278355
Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
Subject does not have a bstampfile, copying /opt/freesurfer/build-stamp.txt
Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds0036
69-fmriprep/sourcedata/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312

     mri_convert /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_MP02312_wf/an

at_fit_wf/anat_validate/sub-MP02312_T1w_noise_corrected_ras_valid.nii /scratch1/03201/jbwexler/openneuro
_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig/001.mgz

    mri_convert /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_MP02312_wf/ana

t_fit_wf/anat_validate/sub-MP02312_T1w_noise_corrected_ras_valid.nii /scratch1/03201/jbwexler/openneuro_
derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig/001.mgz
reading from /node_tmp/work_dir/fmriprep/ds003669_sub-MP02312/fmriprep_23_2_wf/sub_MP02312_wf/an
at_fit_wf/anat_validate/sub-MP02312_T1w_noise_corrected_ras_valid.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep
/sourcedata/freesurfer/sub-MP02312/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri May 3 17:33:13 UTC 2024
Found 1 runs
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.

     cp /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/source

data/freesurfer/sub-MP02312/mri/orig/001.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/
fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz

     mri_info /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/

sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz

    rawavg.mgz ========================================
    Volume information for /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003

669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz
type: MGH
dimensions: 176 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 1
xstart: -88.0, xend: 88.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.0225
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -34.8087

    talairach xfm :
    Orientation   : RAS
    Primary Slice Direction: axial

    voxel to ras transform:
                    1.0000   0.0000   0.0000   -87.5000
                    0.0000   1.0000   0.0000  -110.9775
                    0.0000   0.0000   1.0000  -162.8087
                    0.0000   0.0000   0.0000     1.0000

    voxel-to-ras determinant 1

    ras to voxel transform:
                    1.0000   0.0000   0.0000    87.5000
                    0.0000   1.0000   0.0000   110.9775
                    0.0000   0.0000   1.0000   162.8087
                    0.0000   0.0000   0.0000     1.0000
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312

     mri_convert /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmripr

ep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz /scratch1/03201/jbwexler/openneuro_derivatives/deriv
atives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz --conform

    mri_convert /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmripre

p/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz /scratch1/03201/jbwexler/openneuro_derivatives/deriva
tives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz --conform
reading from /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmripr
ep/sourcedata/freesurfer/sub-MP02312/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 4095 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep
/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz...

     mri_add_xform_to_header -c /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/

ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach.xfm /scratch1/03201/jbwexle
r/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/ori
g.mgz /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/f
reesurfer/sub-MP02312/mri/orig.mgz

    INFO: extension is mgz

     mri_info /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/

sourcedata/freesurfer/sub-MP02312/mri/orig.mgz

    orig.mgz ========================================
    Volume information for /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003

669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 17.0225
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -34.8087

    talairach xfm : /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmr

iprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal

    voxel to ras transform:
                   -1.0000   0.0000   0.0000   128.5000
                    0.0000   0.0000   1.0000  -110.9775
                    0.0000  -1.0000   0.0000    93.1913
                    0.0000   0.0000   0.0000     1.0000

    voxel-to-ras determinant -1

    ras to voxel transform:
                   -1.0000  -0.0000  -0.0000   128.5000
                   -0.0000  -0.0000  -1.0000    93.1913
                   -0.0000   1.0000  -0.0000   110.9775
                   -0.0000  -0.0000  -0.0000     1.0000
    #--------------------------------------------
    #@# Talairach Fri May  3 17:33:20 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000

--distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri May 3 17:33:20 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.279572
cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourced
ata/freesurfer/sub-MP02312/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.279572/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.279572/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.279572/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.279572/nu0.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)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...

    Fri May  3 17:36:41 UTC 2024
    mri_nu_correct.mni done

     talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

    talairach_avi log file is transforms/talairach_avi.log...
    mv -f /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sour

cedata/freesurfer/sub-MP02312/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /scratch1/03201/
jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/
mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
Started at Fri May 3 17:36:41 UTC 2024
Ended at Fri May 3 17:37:01 UTC 2024
talairach_avi done

     cp transforms/talairach.auto.xfm transforms/talairach.xfm

    lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talai

rach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.3.2

    --src: orig.mgz src image (geometry).
    --trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
    --inmni: transforms/talairach.xfm input MNI/XFM transform.
    --outlta: transforms/talairach.xfm.lta output LTA.
    --s: fsaverage subject name
    --ltavox2vox: output LTA as VOX_TO_VOX transform.
     LTA read, type : 1
     0.99830   0.05431   0.01687   0.19576;
    -0.29411   3.32086  -1.84695  -63.01923;
     0.14737  -1.86987   2.62712   39.53989;
     0.00000   0.00000   0.00000   1.00000;
    setting subject to fsaverage
    Writing  LTA to file transforms/talairach.xfm.lta...
    lta_convert successful.
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmripr
ep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

    lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talai

rach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.3.2

    --src: orig.mgz src image (geometry).
    --trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
    --inmni: transforms/talairach.xfm input MNI/XFM transform.
    --outlta: transforms/talairach.xfm.lta output LTA.
    --s: fsaverage subject name
    --ltavox2vox: output LTA as VOX_TO_VOX transform.
     LTA read, type : 1
     0.99830   0.05431   0.01687   0.19576;
    -0.29411   3.32086  -1.84695  -63.01923;
     0.14737  -1.86987   2.62712   39.53989;
     0.00000   0.00000   0.00000   1.00000;
    setting subject to fsaverage
    Writing  LTA to file transforms/talairach.xfm.lta...
    lta_convert successful.
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmripr
ep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri
#--------------------------------------------
#@# Talairach Failure Detection Fri May 3 17:37:03 UTC 2024
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri

     talairach_afd -T 0.005 -xfm transforms/talairach.xfm

    ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval

=0.0000 < threshold=0.0050)

    Manual Talairach alignment may be necessary, or
    include the -notal-check flag to skip this test,
    making sure the -notal-check flag follows -all
    or -autorecon1 in the command string.
    See:

    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

    INFO: Retrying Talairach align using 3T-based atlas...

    #--------------------------------------------
    #@# Talairach Fri May  3 17:37:03 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000

--distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri May 3 17:37:03 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.882
cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourced
ata/freesurfer/sub-MP02312/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.882/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.882/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.882/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.882/nu0.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)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...

    Fri May  3 17:40:23 UTC 2024
    mri_nu_correct.mni done

     talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN3

2_as_orig

    talairach_avi log file is transforms/talairach_avi.log...
    mv -f /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sour

cedata/freesurfer/sub-MP02312/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /scratch1/0
3201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP0
2312/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt
Started at Fri May 3 17:40:24 UTC 2024
Ended at Fri May 3 17:40:43 UTC 2024
talairach_avi done

     cp transforms/talairach.auto.xfm transforms/talairach.xfm

    lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talai

rach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.3.2

    --src: orig.mgz src image (geometry).
    --trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
    --inmni: transforms/talairach.xfm input MNI/XFM transform.
    --outlta: transforms/talairach.xfm.lta output LTA.
    --s: fsaverage subject name
    --ltavox2vox: output LTA as VOX_TO_VOX transform.
     LTA read, type : 1
     0.98975   0.06058   0.03071  -0.51796;
    -0.09829   1.17042   0.16216  -14.36108;
    -0.01288  -0.18079   1.09896   3.51234;
     0.00000   0.00000   0.00000   1.00000;
    setting subject to fsaverage
    Writing  LTA to file transforms/talairach.xfm.lta...
    lta_convert successful.
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmripr
ep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri
#--------------------------------------------
#@# Talairach Failure Detection Fri May 3 17:40:45 UTC 2024
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri

     talairach_afd -T 0.005 -xfm transforms/talairach.xfm

    talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7153, pval=0.4932 >= thresh

old=0.0050)

     awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /scratch1/03201/jbwexler/openneuro_deri

vatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairac
h_avi.log

     tal_QC_AZS /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmripre

p/sourcedata/freesurfer/sub-MP02312/mri/transforms/talairach_avi.log

    TalAviQA: 0.89852
    z-score: -18
    WARNING: Talairach QA check failed!
    z-score of -18 is <= threshold of -9


    Manual Talairach alignment may be necessary, or
    include the -notal-check flag to skip this test,
    making sure the -notal-check flag follows -all
    or -autorecon1 in the command string.
    See:

    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

    INFO: Trying MINC mritotal to perform Talairach align...

    #--------------------------------------------
    #@# Talairach Fri May  3 17:40:45 UTC 2024
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri

     mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000

--distance 50

    /usr/bin/bc
    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri May 3 17:40:45 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.8161
cd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourced
ata/freesurfer/sub-MP02312/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.8161/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.8161/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.8161/nu0.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)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...

    Fri May  3 17:44:05 UTC 2024
    mri_nu_correct.mni done

     talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

    /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata

/freesurfer/sub-MP02312/mri
/opt/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach 7.3.2
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux
Fri May 3 17:44:06 UTC 2024
tmpdir is transforms/tmp.talairach.15126
/scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003669-fmriprep/sourcedata
/freesurfer/sub-MP02312/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.15126/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.15126/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.15126/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protoc
ol icbm transforms/tmp.talairach.15126/src.mnc transforms/talairach.auto.xfm
autocrop: couldn't find program "mincreshape"
Undefined subroutine &main::Fatal called at /opt/freesurfer/mni/bin/autocrop line 171.
mritotal: crashed while running autocrop (termination status=512)
ERROR: mritotal failed, see transforms/talairach.log
Linux c110-191.frontera.tacc.utexas.edu 3.10.0-1160.90.1.el7.x86_64 #1 SMP Thu May 4 15:21:22 UT
C 2023 x86_64 x86_64 x86_64 GNU/Linux

    recon-all -s sub-MP02312 exited with ERRORS at Fri May  3 17:44:07 UTC 2024

    For more details, see the log file /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fm

riprep/ds003669-fmriprep/sourcedata/freesurfer/sub-MP02312/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Stderr:

Traceback:
RuntimeError: subprocess exited with code 1.
@jbwexler jbwexler added the fmriprep Affects fMRIPrep label Jun 3, 2024
@effigies
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effigies commented Jun 4, 2024

Needs mincreshape added to the docker image.

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