Hi everyone,
I encounter an error when using the ciftify_recon_all (version 2.3.3) command on freesurfer (version 7.2.0) recon_all output folder. Command that i use is as follows:
ciftify_recon_all --fs-subjects-dir /mnt/d/Tutorialdata/freesurf/FS/BL --ciftify-work-dir /home/alexlin/test/ciftify sub-218
Here is the log file
cifti_recon_all.txt (17.2 KB)
The last few lines are as follows:
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
I really appreciate your help.
Zhengyu