The full path to the talairach.xfm is saved as part of the mgz volume, which is then accessed when surfaces are loaded. When you change the name of the directory, it still looks in the old directory and does not find what it's looking for. This only creates a problem if you want to get talairach coords. To fix it, you can run something like
cd newfolder/mri mri_add_xform_to_header -c /usr/local/freesurfer/subjects/newfolder/mri/transforms/talairach.xfm \ orig.mgz orig.mgz
You should probably do this for each volume in mri/
doug
Yuhong Jiang wrote:
Hi,
We are running free-surfer dev 2005-10-03 version
I ran "recon-all -subjid [oldfolder] -autorecon1", and subsequently I changed the folder name to [newfolder], and ran "recon-all -subjid [newfolder] -autorecon2".
After that, when I used "tksurfer [newfolder] lh inflated", a warning was given. It says:
WARNING: can't find the talairach xform '/usr/local/freesurfer/subjects/oldfolder/transforms/talairach.xfm' WARNING: transform is not loaded into mri
Could you please let me know why tksurfer is looking for the oldfolder's talairach.xfm? Is there a place that we can change so that it will be looking for the newfolder? Thanks.
--Yuhong
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Yuhong Jiang yuhong@MIT.EDU 617-876-2054 http://web.mit.edu/yuhong/www=============================================================================
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