Hello FreeSurfer Developers,
I'm attempting to run the Human Connectome Project's FreeSurferPipeline.sh script (https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/Fr...) on a test subject, but am encountering the following error during the "WM/GM Contrast lh" step, when pctsurfcon is called:
mri_vol2surf --mov /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/surf/tmp.pctsurfcon.32625/lh.wm.mgh --regheader hcptest8_1mm --cortex No such file or directory mri_vol2surf: could not open label file /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label
... Loading label /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label Invalid argument mri_vol2surf: could not load label file /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label Invalid argument
I looked in the subject's /label/ folder, and only found one file: lh.aparc.annot; furthermore, no right hemisphere files have been created yet.
I've searched the mail archives and no similar errors have been reported. I also tried to backtrack to find out which step of recon-all creates the lh.cortex.label file (is it step 11, "CA Label"?), but instead of finding the step that creates this file, I found commands that used it (i.e., mris_anatomical_stats). Please let me know if I'm approaching this incorrectly. I'm not sure how to proceed from here. I've attached the recon-all.log and recon-all-status.log in case they're of any use.
1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Platform: CentOS 4
3) uname -a: Linux induction.sdsc.edu 2.6.18-419.el5 #1 SMP Fri Feb 24 22:47:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Many thanks,
Anna