Hello,
I asked about this issue about a month ago, but haven't gotten a
response. I'm trying to build a new GCA using the rebuild_gca_atlas.csh
script, with checking disabled (no `-check' flag). My subjects are
completely acallosal, and each of the edited segmentation volumes
that the script wants (seg_edited.mgz) were created by converting the
corresponding aseg.mgz to one-file gzipped NIFTI (aseg.nii.gz), "stamping"
manually-labeled ventricle masks on it, with the command
fslmaths aseg.nii.gz -mul left-lat-inverse-mask.nii.gz -mul
right-lat-inverse-mask.nii.gz -add left-lat-mask-4.nii.gz -add
right-lat-mask-43.nii.gz seg_edited.nii.gz
(here "4" and "43" mean that each of the *-lat-mask-* files contain voxels
with the respective value, based on the entries in FreeSurferColorLUT.txt)
and finally converting the edited segmentation volume back to MNI format
with `mri_convert -odt uchar -ns 1 seg_edited.nii.gz seg_edited.mgz'.
I then copied the seg_edited.mgz into $SUBJECTS_DIR/<subj-id>/mri, and
embedded the talairach transformation matrix in it using
`mri_add_xform_to_header transform/talairach.xfm seg_edited.mgz'.
The first stage of the script worked OK, but the second stage (which
includes a call to mri_ca_train), didn't finish:
============
mri_ca_train using all subjects, using talairach_one.m3z, producing
/Users/j
sm/work/subjects/average/RB_all_2008-12-10.gca...
reading input 0: /Users/jsm/work/subjects/a36/mri/norm.mgz
spacing priors every 2.0 mm
spacing nodes every 4.0 mm
using MR volume brain.mgz to mask input volume...
reading segmentation from subject's mri/seg_edited.mgz directory
reading xform from talairach_one.m3z
reading T1 data from subject's mri/norm.mgz directory
training on 5 subject and writing results to
/Users/jsm/work/subjects/averag
e/RB_all_2008-12-10.gca
***************************************************************************
processing subject a36, 1 of 5...
reading volume /Users/jsm/work/subjects/a36/mri/brain.mgz for masking...
gunzip -c /Users/jsm/work/subjects/a36/mri/transforms/talairach_one.m3z
reading input 0: /Users/jsm/work/subjects/A59/mri/norm.mgz
15129 prior holes filled
***************************************************************************
processing subject A59, 2 of 5...
reading volume /Users/jsm/work/subjects/A59/mri/brain.mgz for masking...
gunzip -c /Users/jsm/work/subjects/A59/mri/transforms/talairach_one.m3z
reading input 0: /Users/jsm/work/subjects/f10/mri/norm.mgz
15304 prior holes filled
***************************************************************************
processing subject f10, 3 of 5...
reading volume /Users/jsm/work/subjects/f10/mri/brain.mgz for masking...
gunzip -c /Users/jsm/work/subjects/f10/mri/transforms/talairach_one.m3z
reading input 0: /Users/jsm/work/subjects/f18/mri/norm.mgz
851 prior holes filled
***************************************************************************
processing subject f18, 4 of 5...
reading volume /Users/jsm/work/subjects/f18/mri/brain.mgz for masking...
gunzip -c /Users/jsm/work/subjects/f18/mri/transforms/talairach_one.m3z
reading input 0: /Users/jsm/work/subjects/f20/mri/norm.mgz
36063 prior holes filled
***************************************************************************
processing subject f20, 5 of 5...
reading volume /Users/jsm/work/subjects/f20/mri/brain.mgz for masking...
gunzip -c /Users/jsm/work/subjects/f20/mri/transforms/talairach_one.m3z
GCAupdateNodeCovariance(21, 33, 6, 42): could not find label
=================
This problem _doesn't_ occur when I only use one subject. Any advice?
Thanks,
Jason
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
