Hello,
I am learning how to use Freesurfer command utilities and I came upon an issue. I have run a subject T1 scan through the recon-all steps and now have my parcel maps. Can someone help direct me on how I can extract individual images for each ROI label in the wmparc.mgz file? I would like to then convert these images to .nii format to read into other software for my analysis. I have performed this process with reading the .mgz into Slicer and doing it by hand(threshold image), but I assume there is a faster, less tedious way to do it using the native commands in Freesurfer. Any help or direction would be greatly appreciated.
Best, Ben -- Benjamin Pruce, R.A. Psychological and Brain Sciences Indiana University Bloomington, IN 47401
Hi Ben,
mri_binarize --match
or
mri_extract_label
will both do the trick (note that if you specify the output name as .nii it will write it to nifti format)
cheers Bruce
On Tue, 26 Jan 2010, Pruce, Benjamin wrote:
Hello,
I am learning how to use Freesurfer command utilities and I came upon an issue. I have run a subject T1 scan through the recon-all steps and now have my parcel maps. Can someone help direct me on how I can extract individual images for each ROI label in the wmparc.mgz file? I would like to then convert these images to .nii format to read into other software for my analysis. I have performed this process with reading the .mgz into Slicer and doing it by hand(threshold image), but I assume there is a faster, less tedious way to do it using the native commands in Freesurfer. Any help or direction would be greatly appreciated.
Best, Ben -- Benjamin Pruce, R.A. Psychological and Brain Sciences Indiana University Bloomington, IN 47401
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Pruce, Benjamin