Node: fmriprep_22_0_wf.single_subject_06_wf.anat_preproc_wf.surface_recon_wf.autorecon1 Working directory: /data/fmriprep/work_dir/fmriprep_22_0_wf/single_subject_06_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/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/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 /data/BIDS/sub-06/anat/sub-06_T1w.nii.gz -noskullstrip -noT2pial -noFLAIRpial -hires -openmp 8 -subjid sub-06 -sd /data/fmriprep/sourcedata/freesurfer -expert /data/fmriprep/work_dir/fmriprep_22_0_wf/single_subject_06_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts Stdout: INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b INFO: SUBJECTS_DIR is /data/fmriprep/sourcedata/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux nautilus 5.15.0-107-generic #117-Ubuntu SMP Fri Apr 26 12:26:49 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux /data/fmriprep/sourcedata/freesurfer/sub-06 mri_convert /data/BIDS/sub-06/anat/sub-06_T1w.nii.gz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig/001.mgz mri_convert /data/BIDS/sub-06/anat/sub-06_T1w.nii.gz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig/001.mgz reading from /data/BIDS/sub-06/anat/sub-06_T1w.nii.gz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999203, -0.0156949, -0.0367063) j_ras = (0.0233705, 0.97542, 0.219112) k_ras = (0.0323651, -0.219795, 0.975009) writing to /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Jul 18 11:41:07 CEST 2024 Found 1 runs /data/fmriprep/sourcedata/freesurfer/sub-06/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 /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig/001.mgz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /data/fmriprep/sourcedata/freesurfer/sub-06 mri_convert /data/fmriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz --conform_min mri_convert /data/fmriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz --conform_min reading from /data/fmriprep/sourcedata/freesurfer/sub-06/mri/rawavg.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999203, -0.0156949, -0.0367063) j_ras = (0.0233705, 0.97542, 0.219112) k_ras = (0.0323651, -0.219795, 0.975009) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4085 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz... mri_add_xform_to_header -c /data/fmriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach.xfm /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz /data/fmriprep/sourcedata/freesurfer/sub-06/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Jul 18 11:41:32 CEST 2024 /data/fmriprep/sourcedata/freesurfer/sub-06/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 /data/fmriprep/sourcedata/freesurfer/sub-06/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 7.2.0 Linux nautilus 5.15.0-107-generic #117-Ubuntu SMP Fri Apr 26 12:26:49 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 18 11:41:32 CEST 2024 tmpdir is ./tmp.mri_nu_correct.mni.604502 cd /data/fmriprep/sourcedata/freesurfer/sub-06/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.604502/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.604502/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.604502/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.604502/nu0.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.16402e-10, -2.86561e-09) j_ras = (2.86561e-09, 0, -1) k_ras = (-7.16402e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Thu Jul 18 11:49:18 CEST 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... Started at Thu Jul 18 11:49:20 CEST 2024 Ended at Thu Jul 18 11:49:55 CEST 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 7.2.0 --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 1.27830 -0.07062 -0.02792 -4.15817; 0.08257 1.06935 0.28636 -34.69358; 0.03503 -0.22377 1.19210 19.37392; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /data/fmriprep/sourcedata/freesurfer/sub-06/mri/transforms /data/fmriprep/sourcedata/freesurfer/sub-06/mri /data/fmriprep/sourcedata/freesurfer/sub-06/mri #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 18 11:49:58 CEST 2024 /data/fmriprep/sourcedata/freesurfer/sub-06/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7627, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /data/fmriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach_avi.log tal_QC_AZS /data/fmriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach_avi.log TalAviQA: 0.96436 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 18 11:49:58 CEST 2024 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 /usr/bin/bc /data/fmriprep/sourcedata/freesurfer/sub-06/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.2.0 Linux nautilus 5.15.0-107-generic #117-Ubuntu SMP Fri Apr 26 12:26:49 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 18 11:49:58 CEST 2024 tmpdir is ./tmp.mri_nu_correct.mni.631428 cd /data/fmriprep/sourcedata/freesurfer/sub-06/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.631428/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.631428/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.631428/ones.mgz 7.2.0 cwd /data/fmriprep/sourcedata/freesurfer/sub-06/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.631428/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.631428/ones.mgz sysname Linux hostname nautilus machine x86_64 user dc277359 input ./tmp.mri_nu_correct.mni.631428/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.631428/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 32768000 values in range Counting number of voxels in first frame Found 32767999 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.631428/ones.mgz Count: 32767999 8998910.858188 32768000 99.999997 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.631428/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.631428/sum.junk --avgwf ./tmp.mri_nu_correct.mni.631428/input.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.631428/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.631428/sum.junk --avgwf ./tmp.mri_nu_correct.mni.631428/input.mean.dat sysname Linux hostname nautilus machine x86_64 user dc277359 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.631428/ones.mgz Loading orig.mgz Voxel Volume is 0.274625 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.631428/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.631428/ones.mgz --i ./tmp.mri_nu_correct.mni.631428/nu0.mgz --sum ./tmp.mri_nu_correct.mni.631428/sum.junk --avgwf ./tmp.mri_nu_correct.mni.631428/output.mean.dat 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.631428/ones.mgz --i ./tmp.mri_nu_correct.mni.631428/nu0.mgz --sum ./tmp.mri_nu_correct.mni.631428/sum.junk --avgwf ./tmp.mri_nu_correct.mni.631428/output.mean.dat sysname Linux hostname nautilus machine x86_64 user dc277359 whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.631428/ones.mgz Loading ./tmp.mri_nu_correct.mni.631428/nu0.mgz Voxel Volume is 0.274625 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.631428/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.631428/nu0.mgz ./tmp.mri_nu_correct.mni.631428/nu0.mgz mul .88542000470814539840 Saving result to './tmp.mri_nu_correct.mni.631428/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.631428/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.631428/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.631428/nu0.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.16402e-10, -2.86561e-09) j_ras = (2.86561e-09, 0, -1) k_ras = (-7.16402e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping ( 7, 226) to ( 3, 110) Thu Jul 18 11:58:15 CEST 2024 mri_nu_correct.mni done mri_add_xform_to_header -c /data/fmriprep/sourcedata/freesurfer/sub-06/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Jul 18 11:58:17 CEST 2024 /data/fmriprep/sourcedata/freesurfer/sub-06/mri mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.27830 -0.07062 -0.02792 -4.15817; 0.08257 1.06935 0.28636 -34.69358; 0.03503 -0.22377 1.19210 19.37392; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points\00 error: No such file or directory error: MRInormFindControlPoints failed\00 Linux nautilus 5.15.0-107-generic #117-Ubuntu SMP Fri Apr 26 12:26:49 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-06 exited with ERRORS at Thu Jul 18 11:58:31 CEST 2024 For more details, see the log file /data/fmriprep/sourcedata/freesurfer/sub-06/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.