mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template?
On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
Dear FreeSurfer experts,
I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line. I have tried mri_mask as well but do not think it is the command to go. I also checked if two volumes are in the same orientation using mri_orient.
mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
- (I have the native oriented version of this volume template as well,
and I attached a photo of the template as well)
I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help
Idil
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