Hello Freesurfer list,
I have several different surface labels that I am converting into volume regions-of-interest in white matter. For 2 out of 11 participants, one of the labels will not convert. My command has worked for these two participants with all other labels that I've tried. I have no trouble viewing the label in question on the inflated surface with freeview, and no problem viewing the brain.mgz files.
Ideas? Thank you, Martha
Command:
mri_label2vol --label d16/roi_lh_man3/lh.behav-full-sig2-transformed.label --temp ~/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz --reg d16/reg/surf2conf.dat --subject d16 --hemi lh --proj abs -1 -1 0.1 --o d16/roi_lh_man3/roi_lh_man3_conf.nii.gz; done
Output:
Number of labels: 1 d16/roi_lh_man3/lh.behav-full-sig2-transformed.label Annot File: (null) Template Volume: /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz Outut Volume: d16/roi_lh_man3/roi_lh_man3_conf.nii.gz Registration File: d16/reg/surf2conf.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: abs ProjTypeId: 1 ProjStart: -1 ProjStop: -1 ProjDelta: 0.1 Subject: d16 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Loading registration from d16/reg/surf2conf.dat RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.white nvertices = 114782 Reading thickness /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.thickness nlabels = 1 Allocating Hit Volume (16777216) voxels Loading d16/roi_lh_man3/lh.behav-full-sig2-transformed.label Segmentation fault