Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

Thank you. I succeeded to convert it, but the label is completely incorrect. Actually, I can not understand how exactly it can work: when I make an opposite direction with mri_label2vol I pass the registrer.dat file; however, in mri_cor2label there is no such option. How then this transformation can be achieved?

On Mon, Apr 12, 2010 at 7:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

The id is the value in the mask. So if it's a binary mask, use --id 1

John Gelburg wrote:

...

I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM.

On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It will still work.

from mri_cor2label --help :

Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc).

John Gelburg wrote:

   thanks, but isn't COR volume and my ANALYZE image is not the
   same thing?

   On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve
   <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
   <mailto:greve@nmr.mgh.harvard.edu
   <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

      try mri_cor2label

      John Gelburg wrote:

          Hi,

          I have ANLYZE binary mask which I would like to convert to
          FreeSurfer labels. Is there any more automatic way to do it
          than loading it as an overlay and then selecting
   manually as a
          label?

          Thanks for help,
          John

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html