You are right, it turned out there was an issue with $SUBJECTS_DIR and when I fixed it, everything worked fine.
Thank you very much for your help!
Peter
On 09/16/2011 03:22 PM, Douglas N Greve wrote:
Is that subject in your $SUBJECTS_DIR ?
Peter Savadjiev wrote:
Hi Douglas,
I removed the --surf curv option from the command, but had exactly the same error output.
Also, if curv is not a surface, how can I get the curvature values into a 3D volume? This is all I'm really interested in.
Thank you once again,
Peter
On 09/16/2011 02:39 PM, Douglas N Greve wrote:
Oh, don't use --surf curv. The curv is not a surface (which has vertex XYZ and neighborhood relationships). Leave that option off (to get white) or specify a real surface. doug
Peter Savadjiev wrote:
Hi Douglas,
Yes, I know that, I just put subjid in the email not to enter a long pathname and an actual subject id that is irrelevant to the email. Sorry about the confusion. Do you see any other problem with the command?
Thank you, Peter
On 09/16/2011 02:22 PM, Douglas N Greve wrote:
subjid should be the name of your subject (not literally "subjid")
Peter Savadjiev wrote:
Hi,
I am trying to convert the "curv" surfaces to a volume, using the mri_surf2vol command in the following manner:
cd subjects/subjid mri_surf2vol --surf curv --hemi lh --template ./mri/orig.mgz --outvol /tmp/curv.mgz --surfval ./surf/lh.curv --fillribbon --volregidentity subjid
I get the following output: gdiagno = -1 Using identity matrix for registration Cannot find orig.mgz, trying orig/COR files instead... mri_read(): couldn't determine type of file subjects/subjid/mri/orig mri_surf2vol ERROR: reading subjects/subjid/mri/orig header
Could you please tell me what is wrong with the command? In particular, the file orig.mgz does exist at the specified path, so I don't understand why "cannot find orig.mgz"? The file can be visualized without problems, so the file is not corrupted.
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