Hi Qizhu, I don't remember what your previous email was about. If you are just going to map the thickness values to a volume in the subject's conformed anatomical space, then you can just specify "--subject subjectname". --surfval takes the path to the thickness file, eg, $SUBJECTS_DIR/subjectname/surf/lh.thickness. You don't need --template with the --subject above.

doug

On 12/15/10 4:26 AM, qizhu wu wrote:

Dear all,

Continue with my previous question in "To use the file thickness.mgh outside Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to convert mgh files into image format, such as NIFTI.
But I failed due to wrong setting on several arguments:

1, '--volreg': I do not understand what file it requires. It's declared in --help that "Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume". But I am only dealing with the structural volumes, and has this file been created in any step during the previous processing? Or could anyone tell me clearly how to set this argument?

2, --surfval: if only pthname rather than single file is allowed as input here?

3, --template: couldI use mni305.cor.mgz, or just left these optional arguments empty?

thanks in advance.

Qizhu Wu
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