Hello,
I'm trying to use anatomical regions of a subject labeled by freesurfer as an fMRI mask in brainvoyager. I'm using mri_convert to change aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr file.
However, the vmr file in brainvoyager looks wrong (see attached screenshot).
My conversion command is "mri_convert --in_type mgz --out_type nii --input_volume aparc+aseg.mgz --output_volume aparc+aseg.nii".
Has anyone successfully imported freesurfer segmentation volumes to use as masks in branvoyager? Any advice would be greatly appreciated. Thanks!
-Dave
[image: Inline image 1]
I've never used BV, so I can't help you. You might want to contact the BV folks as they may have more experience in this. best doug
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm trying to use anatomical regions of a subject labeled by freesurfer as an fMRI mask in brainvoyager. I'm using mri_convert to change aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr file.
However, the vmr file in brainvoyager looks wrong (see attached screenshot).
My conversion command is "mri_convert --in_type mgz --out_type nii --input_volume aparc+aseg.mgz --output_volume aparc+aseg.nii".
Has anyone successfully imported freesurfer segmentation volumes to use as masks in branvoyager? Any advice would be greatly appreciated. Thanks!
-Dave
Inline image 1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
btw, if I had to guess, I'd say it is an "endianness" problem.
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm trying to use anatomical regions of a subject labeled by freesurfer as an fMRI mask in brainvoyager. I'm using mri_convert to change aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr file.
However, the vmr file in brainvoyager looks wrong (see attached screenshot).
My conversion command is "mri_convert --in_type mgz --out_type nii --input_volume aparc+aseg.mgz --output_volume aparc+aseg.nii".
Has anyone successfully imported freesurfer segmentation volumes to use as masks in branvoyager? Any advice would be greatly appreciated. Thanks!
-Dave
Inline image 1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Dave Frank -
Douglas Greve