Re: [Freesurfer] convert from MNI152 to native space

Try now

On 06/15/2016 06:30 PM, Leila Reddy wrote:

Hi Doug,

Thanks for your reply.

When I run mni152reg I get an error : ERROR: Flag --lta unrecognized

I'm using v 1.9 of this file.

I found a post that said to download a newer version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

but it doesn't seem to be there anymore.

Thanks, Leila

On Wednesday, June 15, 2016 11:55 AM, Leila Reddy leils@yahoo.com wrote:

Hi,

I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview:

mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg

The overlay of the mask on f.nii in Freeview is mostly outside the brain.

How can I go about this step?

Thanks for your help, Leila

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer