.|'; || .|'; '' || || '' || .|'', || '||' ''||'' || '||' '|| ||` || || || || || || `|..|| `|..' .||. .||. `|..' .||. .||. || , |' '' ------------------------------------------------------------- 2022-06-17 11:50:16.357661 : Starting cifti_recon_all ------------------------------------------------------------- Creating tempdir:/tmp/tmpwnq92wv4 on host:alexlin-Precision-7550 Arguments: freesurfer SUBJECTS_DIR: /mnt/d/Tutorialdata/freesurf/FS/BL CIFTIFY_WORKDIR directory: /home/alexlin/test/ciftify Subject: sub-218 MSM config file: /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/MSMSulcStrainFinalconf ---### Environment Settings ###--- Username: alexlin System Info: OS: Linux Hostname: alexlin-Precision-7550 Release: 5.4.0-117-generic Version: #132~18.04.1-Ubuntu SMP Thu Jun 2 23:36:48 UTC 2022 Machine: x86_64 ciftify: Version: 2.3.3 wb_command: Path: /home/alexlin/Documents/Toolbox/workbench/bin_linux64/wb_command Version: 1.5.0 Commit Date: 2021-02-16 13:46:47 -0600 Operating System: Linux freesurfer: Path: /usr/local/freesurfer/7.2.0/bin Build Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b FSL: Path: /usr/local/fsl Version: 6.0.5.1:57b01774 ---### End of Environment Settings ###--- recon_all was run 2022年 03月 03日 星期四 07:58:49 CST with settings: Build Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Version parsed as: unknown CMD args: -s sub-218_ses-BL_T1w -i sub-218_ses-BL_T1w.nii -all -qcache ------------------------------------------------------------- 2022-06-17 11:50:16.404745 : Converting T1wImage and Segmentations from freesurfer ------------------------------------------------------------- Running: mri_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/T1.mgz /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz mri_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/T1.mgz /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz reading from /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/T1.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -6.1118e-10, 0) j_ras = (0, 0, -1) k_ras = (2.48838e-09, 1, 0) writing to /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz... Running: fslreorient2std /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz Running: mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/wmparc.mgz /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/wmparc.mgz /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz reading from /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/wmparc.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -6.1118e-10, 0) j_ras = (0, 0, -1) k_ras = (2.48838e-09, 1, 0) reading template info from volume /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz... changing data type from int to uchar (noscale = 0)... MRIchangeType: Building histogram 0 5002 1000, flo=0, fhi=0.999, dest_type=0 MRIcopyHeader(): source has ctab Reslicing using nearest writing to /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz... Running: wb_command -logging SEVERE -volume-label-import /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz -drop-unused-labels Running: mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc.a2009s+aseg.mgz /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc.a2009s+aseg.mgz /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz reading from /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc.a2009s+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -6.1118e-10, 0) j_ras = (0, 0, -1) k_ras = (2.48838e-09, 1, 0) reading template info from volume /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz... changing data type from int to uchar (noscale = 0)... MRIchangeType: Building histogram 0 12175 1000, flo=0, fhi=0.999, dest_type=0 MRIcopyHeader(): source has ctab Reslicing using nearest writing to /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz... Running: wb_command -logging SEVERE -volume-label-import /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz -drop-unused-labels Running: mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc+aseg.mgz /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz mri_convert -rt nearest -rl /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc+aseg.mgz /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz reading from /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -6.1118e-10, 0) j_ras = (0, 0, -1) k_ras = (2.48838e-09, 1, 0) reading template info from volume /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz... changing data type from int to uchar (noscale = 0)... MRIchangeType: Building histogram 0 2035 1000, flo=0, fhi=0.999, dest_type=0 MRIcopyHeader(): source has ctab Reslicing using nearest writing to /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz... Running: wb_command -logging SEVERE -volume-label-import /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz -drop-unused-labels ------------------------------------------------------------- 2022-06-17 11:50:30.478100 : Creating brainmask from freesurfer wmparc segmentation ------------------------------------------------------------- Running: fslmaths /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz -bin -dilD -dilD -dilD -ero -ero /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz Running: wb_command -volume-fill-holes /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz Running: fslmaths /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz -bin /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz Running: fslmaths /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz -mul /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz /home/alexlin/test/ciftify/sub-218/T1w/T1w_brain.nii.gz ------------------------------------------------------------- 2022-06-17 11:51:16.535432 : Registering T1wImage to MNI template using FSL FNIRT ------------------------------------------------------------- Running: flirt -interp spline -dof 12 -in /home/alexlin/test/ciftify/sub-218/T1w/T1w_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -omat /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /tmp/tmpwnq92wv4/T1w2StandardLinearImage.nii.gz Running: fnirt --in=/tmp/tmpwnq92wv4/T1w2StandardLinearImage.nii.gz --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --refmask=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz --fout=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --logout=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/NonlinearReg_fromlinear.log --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf Running: invwarp -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/Standard2T1w_warp_noaffine.nii.gz -r /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz Running: applywarp --rel --interp=trilinear -i /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz -r /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz ------------------------------------------------------------- 2022-06-17 12:00:34.043181 : Applying MNI transform to label files ------------------------------------------------------------- Running: applywarp --rel --interp=nn -i /home/alexlin/test/ciftify/sub-218/T1w/wmparc.nii.gz -r /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/wmparc.nii.gz Running: wb_command -volume-label-import -logging SEVERE /home/alexlin/test/ciftify/sub-218/MNINonLinear/wmparc.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/MNINonLinear/wmparc.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /home/alexlin/test/ciftify/sub-218/T1w/aparc.a2009s+aseg.nii.gz -r /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc.a2009s+aseg.nii.gz Running: wb_command -volume-label-import -logging SEVERE /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc.a2009s+aseg.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc.a2009s+aseg.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /home/alexlin/test/ciftify/sub-218/T1w/aparc+aseg.nii.gz -r /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc+aseg.nii.gz Running: wb_command -volume-label-import -logging SEVERE /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc+aseg.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /home/alexlin/test/ciftify/sub-218/MNINonLinear/aparc+aseg.nii.gz -drop-unused-labels Running: applywarp --rel --interp=nn -i /home/alexlin/test/ciftify/sub-218/T1w/brainmask_fs.nii.gz -r /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz -w /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz --premat=/home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat -o /home/alexlin/test/ciftify/sub-218/MNINonLinear/brainmask_fs.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.native.wb.spec INVALID /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.native.wb.spec INVALID /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/MNINonLinear/sub-218.164k_fs_LR.wb.spec INVALID /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/MNINonLinear/fsaverage_LR32k/sub-218.32k_fs_LR.wb.spec INVALID /home/alexlin/test/ciftify/sub-218/MNINonLinear/T1w.nii.gz Running: mkdir -p /home/alexlin/test/ciftify/zz_templates Running: cp /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz /home/alexlin/test/ciftify/zz_templates/Atlas_ROIs.2.nii.gz Running: applywarp --interp=nn -i /home/alexlin/test/ciftify/sub-218/MNINonLinear/wmparc.nii.gz -r /home/alexlin/test/ciftify/sub-218/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o /tmp/tmpwnq92wv4/wmparc.2.nii.gz Running: wb_command -logging SEVERE -volume-label-import /tmp/tmpwnq92wv4/wmparc.2.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferAllLut.txt /tmp/tmpwnq92wv4/wmparc.2.nii.gz -drop-unused-labels Running: wb_command -logging SEVERE -volume-label-import /tmp/tmpwnq92wv4/wmparc.2.nii.gz /home/alexlin/.local/lib/python3.6/site-packages/ciftify/data/hcp_config/FreeSurferSubcorticalLabelTableLut.txt /home/alexlin/test/ciftify/sub-218/MNINonLinear/ROIs/ROIs.2.nii.gz -discard-others ------------------------------------------------------------- 2022-06-17 12:00:42.140870 : Converting freesurfer surfaces to gifti ------------------------------------------------------------- Evaluating: mri_info /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/mri/brain.finalsurfs.mgz Running: mris_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/surf/lh.white /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii Saving /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii as a surface Running: wb_command -set-structure /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii CORTEX_LEFT -surface-type ANATOMICAL -surface-secondary-type GRAY_WHITE Running: wb_command -surface-apply-affine /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii /tmp/tmpwnq92wv4/cras.mat /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.native.wb.spec CORTEX_LEFT /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii Running: mris_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/surf/rh.white /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii Saving /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii as a surface Running: wb_command -set-structure /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii CORTEX_RIGHT -surface-type ANATOMICAL -surface-secondary-type GRAY_WHITE Running: wb_command -surface-apply-affine /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii /tmp/tmpwnq92wv4/cras.mat /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.native.wb.spec CORTEX_RIGHT /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii Running: wb_command -surface-apply-affine /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.white.native.surf.gii /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.L.white.native.surf.gii -flirt /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz Running: wb_command -surface-apply-warpfield /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.L.white.native.surf.gii /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/Standard2T1w_warp_noaffine.nii.gz /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.L.white.native.surf.gii -fnirt /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.native.wb.spec CORTEX_LEFT /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.L.white.native.surf.gii Running: wb_command -surface-apply-affine /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.R.white.native.surf.gii /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2StandardLinear.mat /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.R.white.native.surf.gii -flirt /home/alexlin/test/ciftify/sub-218/T1w/T1w.nii.gz /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz Running: wb_command -surface-apply-warpfield /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.R.white.native.surf.gii /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/Standard2T1w_warp_noaffine.nii.gz /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.R.white.native.surf.gii -fnirt /home/alexlin/test/ciftify/sub-218/MNINonLinear/xfms/T1w2Standard_warp_noaffine.nii.gz Running: wb_command -add-to-spec-file /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.native.wb.spec CORTEX_RIGHT /home/alexlin/test/ciftify/sub-218/MNINonLinear/Native/sub-218.R.white.native.surf.gii Running: mris_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/surf/lh.pial /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.pial.native.surf.gii cmd: mris_convert /mnt/d/Tutorialdata/freesurf/FS/BL/sub-218/surf/lh.pial /home/alexlin/test/ciftify/sub-218/T1w/Native/sub-218.L.pial.native.surf.gii Failed with returncode 139 ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0