Node: fmriprep_23_1_wf.single_subject_ut0006_wf.anat_preproc_wf.surface_recon_wf.autorecon1 Working directory: /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_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 = 8 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", 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 autorecon1. Cmdline: recon-all -autorecon1 -i /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-ut0006_ses-01_rec-origDefaced_T1w_noise_corrected.nii.gz -noskullstrip -noT2pial -noFLAIRpial -hires -openmp 8 -subjid sub-ut0006 -sd /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer -expert /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts Stdout: INFO: hi-res volumes are conformed to the min voxel size fs-check-version --s sub-ut0006 --o /tmp/tmp.eS0i6M Mon Oct 2 15:24:46 CDT 2023 setenv SUBJECTS_DIR /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer cd /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/surface_recon_wf/autorecon1 /opt/freesurfer/bin/fs-check-version --s sub-ut0006 --o /tmp/tmp.eS0i6M -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 c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux pid 1967698 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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006 mri_convert /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-ut0006_ses-01_rec-origDefaced_T1w_noise_corrected.nii.gz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig/001.mgz mri_convert /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-ut0006_ses-01_rec-origDefaced_T1w_noise_corrected.nii.gz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig/001.mgz reading from /scratch/06950/jalmeida/work/project_nndcbipolar/fmriprep_23_1_wf/single_subject_ut0006_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-ut0006_ses-01_rec-origDefaced_T1w_noise_corrected.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999678, 0.021897, 0.0128457) j_ras = (-0.0222574, 0.999343, 0.0286171) k_ras = (-0.0122106, -0.0288938, 0.999508) writing to /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Oct 2 15:24:59 CDT 2023 Found 1 runs /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig/001.mgz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz mri_info /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz type: MGH dimensions: 192 x 256 x 256 voxel sizes: 0.900000, 0.937500, 0.937500 type: FLOAT (3) fov: 240.000 dof: 1 xstart: -86.4, xend: 86.4 ystart: -120.0, yend: 120.0 zstart: -120.0, zend: 120.0 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 = 0.9997, y_r = -0.0223, z_r = -0.0122, c_r = 3.2470 : x_a = 0.0219, y_a = 0.9993, z_a = -0.0289, c_a = -4.8403 : x_s = 0.0128, y_s = 0.0286, z_s = 0.9995, c_s = -43.1005 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.8997 -0.0209 -0.0114 -78.9890 0.0197 0.9369 -0.0271 -123.1860 0.0116 0.0268 0.9370 -167.5854 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.791016 ras to voxel transform: 1.1108 0.0243 0.0143 93.1263 -0.0237 1.0660 0.0305 134.5523 -0.0130 -0.0308 1.0661 173.8444 0.0000 0.0000 0.0000 1.0000 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006 mri_convert /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz --conform_min mri_convert /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz --conform_min reading from /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999678, 0.021897, 0.0128457) j_ras = (-0.0222574, 0.999343, 0.0286171) k_ras = (-0.0122106, -0.0288938, 0.999508) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram -0.00112578 2848.55 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz... mri_add_xform_to_header -c /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms/talairach.xfm /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz INFO: extension is mgz mri_info /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz orig.mgz ======================================== Volume information for /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/orig.mgz type: MGH dimensions: 266 x 266 x 266 voxel sizes: 0.900000, 0.900000, 0.900000 type: UCHAR (0) fov: 239.400 dof: 1 xstart: -119.7, xend: 119.7 ystart: -119.7, yend: 119.7 zstart: -119.7, zend: 119.7 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 = 3.2470 : x_a = -0.0000, y_a = -0.0000, z_a = 1.0000, c_a = -4.8403 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -43.1006 talairach xfm : /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.9000 0.0000 -0.0000 122.9470 -0.0000 -0.0000 0.9000 -124.5403 0.0000 -0.9000 0.0000 76.5994 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.729 ras to voxel transform: -1.1111 -0.0000 0.0000 136.6078 -0.0000 0.0000 -1.1111 85.1105 -0.0000 1.1111 -0.0000 138.3781 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Mon Oct 2 15:25:07 CDT 2023 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 2 15:25:07 CDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.1968073 cd /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1968073/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.1968073/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.1968073/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.1968073/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.82077e-10, 0) j_ras = (0, -2.06961e-09, -1) k_ras = (-1.48753e-09, 1, 2.06961e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Oct 2 15:28:19 CDT 2023 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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Mon Oct 2 15:28:19 CDT 2023 Ended at Mon Oct 2 15:28:35 CDT 2023 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 1.08851 -0.00908 0.05654 0.20193; -0.29972 1.99235 -0.64798 3.63071; 0.19208 -1.18027 1.97839 11.27591; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 2 15:28:37 CDT 2023 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 Mon Oct 2 15:28:37 CDT 2023 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 2 15:28:37 CDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.2135348 cd /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2135348/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2135348/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2135348/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2135348/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.82077e-10, 0) j_ras = (0, -2.06961e-09, -1) k_ras = (-1.48753e-09, 1, 2.06961e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Oct 2 15:31:44 CDT 2023 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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt Started at Mon Oct 2 15:31:44 CDT 2023 Ended at Mon Oct 2 15:32:00 CDT 2023 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 1.25181 0.93191 -0.07308 -20.00084; -5.09074 33.70058 -7.51070 -680.46191; -3.61703 24.63976 -2.86886 -491.76978; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri/transforms /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 2 15:32:02 CDT 2023 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Mon Oct 2 15:32:02 CDT 2023 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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 c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 2 15:32:02 CDT 2023 tmpdir is ./tmp.mri_nu_correct.mni.2135725 cd /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.2135725/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.2135725/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.2135725/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.2135725/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.82077e-10, 0) j_ras = (0, -2.06961e-09, -1) k_ras = (-1.48753e-09, 1, 2.06961e-09) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Mon Oct 2 15:35:08 CDT 2023 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri /opt/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach 7.3.2 Linux c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 2 15:35:08 CDT 2023 tmpdir is transforms/tmp.talairach.2135925 /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri mri_convert orig_nu.mgz transforms/tmp.talairach.2135925/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.2135925/src.mnc reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.82077e-10, 0) j_ras = (0, -2.06961e-09, -1) k_ras = (-1.48753e-09, 1, 2.06961e-09) writing to transforms/tmp.talairach.2135925/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.2135925/src.mnc transforms/talairach.auto.xfm mritotal: Command not found. ERROR: mritotal failed, see transforms/talairach.log Linux c307-010.ls6.tacc.utexas.edu 4.18.0-372.26.1.el8_6.x86_64 #1 SMP Tue Sep 13 18:09:48 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-ut0006 exited with ERRORS at Mon Oct 2 15:35:09 CDT 2023 For more details, see the log file /work/06950/jalmeida/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/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.