ds004009-fmriprep- "error: GCAhistoScaleImageIntensities: could not find wm peak^@"

[jbwexler]

Just sub-17:

Working directory: /node_tmp/work_dir/fmriprep/ds004009_sub-17/fmriprep_23_2_wf/sub_17_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/gcareg

Node inputs:

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

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 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 gcareg.

Cmdline:
        recon-all -openmp 7 -subjid sub-17 -sd /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer -gcareg
Stdout:
        fs-check-version --s sub-17 --o /tmp/tmp.AJmjlf
        Wed Jun  5 08:19:24 UTC 2024

        setenv SUBJECTS_DIR /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer
        cd /node_tmp/work_dir/fmriprep/ds004009_sub-17/fmriprep_23_2_wf/sub_17_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/gcareg
        /opt/freesurfer/bin/fs-check-version --s sub-17 --o /tmp/tmp.AJmjlf
        -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 c208-016.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 146123
        Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
        bstampfile exists /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17/scripts/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/ds004009-fmriprep/sourcedata/freesurfer
        Actual FREESURFER_HOME /opt/freesurfer
        -rw-r--r-- 1 jbwexler G-802037 121068 Apr 30 13:18 /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17/scripts/recon-all.log
        Linux c208-016.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
        /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17/mri/transforms /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17
        /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17
        #-------------------------------------
        #@# EM Registration Wed Jun  5 08:19:28 UTC 2024
        /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17/mri

         mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2020-01-02.gca transforms/talairach.lta

        setting unknown_nbr_spacing = 3
        using MR volume brainmask.mgz to mask input volume...

        == Number of threads available to mri_em_register for OpenMP = 7 ==
        reading 1 input volumes...
        logging results to talairach.log
        reading '/opt/freesurfer/average/RB_all_2020-01-02.gca'...
        GCAread took 0 minutes and 1 seconds.
        average std = 7.2   using min determinant for regularization = 5.2
        0 singular and 884 ill-conditioned covariance matrices regularized
        reading 'nu.mgz'...
        MRImask(): AllowDiffGeom = 1
        MRImask(): AllowDiffGeom = 1
        MRImask(): AllowDiffGeom = 1
        MRImask(): AllowDiffGeom = 1
        MRImask(): AllowDiffGeom = 1
        freeing gibbs priors...done.
        accounting for voxel sizes in initial transform
        bounding unknown intensity as < 5.9 or > 519.0
        total sample mean = 79.1 (1017 zeros)
        ************************************************
        spacing=8, using 2841 sample points, tol=1.00e-05...
        ************************************************
        register_mri: find_optimal_transform
        find_optimal_transform: nsamples 2841, passno 0, spacing 8
        resetting wm mean[0]: 98 --> 107
        resetting gm mean[0]: 61 --> 61
        input volume #1 is the most T1-like
        using real data threshold=22.0
        skull bounding box = (64, 43, 28) --> (197, 173, 176)
        finding center of left hemi white matter
        using (108, 86, 102) as brain centroid of Right_Cerebral_White_Matter...
        MRImask(): AllowDiffGeom = 1
        mean wm in atlas = 107, using box (92,70,84) --> (124, 101,120) to find MRI wm
        before smoothing, mri peak at 70
        robust fit to distribution - 72 +- 7.9
        distribution too broad for accurate scaling - disabling
        WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=103, mri_peak=107
        after smoothing, mri peak at 0, scaling input intensities by inf
        error: Numerical result out of range
        error: GCAhistoScaleImageIntensities: could not find wm peak^@
        Linux c208-016.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

        recon-all -s sub-17 exited with ERRORS at Wed Jun  5 08:19:46 UTC 2024

        For more details, see the log file /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004009-fmriprep/sourcedata/freesurfer/sub-17/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.