Open jbwexler opened 3 weeks ago
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.
Just sub-17: