Sorry for the delay. Answers below
On 12/21/2015 03:58 PM, Woo, Jonghye wrote:
Dear Doug,
I have following questions: I posted the question but no one answered it.
- What is the best way to convert annotation to the segmentation mask
(volume)?
mri_label2vol. Specify the annotation with the --annot flag. Run with --help to get more help.
- I also asked the questions below.
I tried to use PALS B12 mask in fsaverage, and try to create a volume mask (from the annot file). I used the command below: mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt I’ve got the table from this command: mis_info lh.PALS_B12_Brodmann.annot & mis_info rh.PALS_B12_Brodmann.annot (https://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12) After creating the mask, I compared the table and the mask but they are not corresponding. Rather the labels in the segmentation mask was corresponding to FreeSurferColorLUT.txt.
How are you viewing this? If in tkmedit or freeview, are you specifying a color table?
Do you have any suggestions? Thank you in advance.
Best, Jonghye
On Dec 21, 2015, at 11:50 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Jonghye, is this something that can be handled over email? Is is something that cannot be posted to the list? doug
On 12/16/2015 11:08 AM, Woo, Jonghye wrote:
Dear Doug,
My name is Jonghye and I have a quick question in freesurfer. Can I drop by your office for get some information this afternoon? Looking forward to hearing from you.
Best, Jonghye
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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