Dear Freesurfers,
I have some binary ROI masks of MT/V5 that I’ve drawn from activation maps in fslview, which I would like to transform into labels so that I can project them onto a surface and flat patch.
I have been following parts of this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html
and have tried using mri_vol2surf and mri_cor2label, but I cannot view the result either with tksurfer or freeview. I would like to be able to load the subjects inflated surface with tksurfer, and add the mask as a label, or something similar.
The commands I’ve used are as follows:
mri_vol2surf —src MST_L_bin.nii.gz —out MST_L_surf.mgh —out_type mgh —hemi lh —srcreg MST_L_to_BGimage.dat —projdist 0.5 —ref MST_L_bin.nii.gz
mri_cor2label —i MST_L_surf.mgh --id 1 —l lh.mst.label
I previously created MST_L_to_BGimage using fslregister. I am also attaching the input mask file as well as the label file that I generated in this way.
Are these the right programs to use in this case, and if so, what is the appropriate way of using them?
Thank you in advance for any help.
Sincerely, Niia
You need to include a --surf arg to mri_cor2label. Look at the --help
On 12/15/2016 09:41 AM, Niia Nikolova wrote:
Dear Freesurfers,
I have some binary ROI masks of MT/V5 that I’ve drawn from activation maps in fslview, which I would like to transform into labels so that I can project them onto a surface and flat patch.
I have been following parts of this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32468.html
and have tried using mri_vol2surf and mri_cor2label, but I cannot view the result either with tksurfer or freeview. I would like to be able to load the subjects inflated surface with tksurfer, and add the mask as a label, or something similar.
The commands I’ve used are as follows:
mri_vol2surf —src MST_L_bin.nii.gz —out MST_L_surf.mgh —out_type mgh —hemi lh —srcreg MST_L_to_BGimage.dat —projdist 0.5 —ref MST_L_bin.nii.gz
mri_cor2label —i MST_L_surf.mgh --id 1 —l lh.mst.label
I previously created MST_L_to_BGimage using fslregister. I am also attaching the input mask file as well as the label file that I generated in this way.
Are these the right programs to use in this case, and if so, what is the appropriate way of using them?
Thank you in advance for any help.
Sincerely, Niia
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Niia Nikolova