You'll need a registration that goes from the functional to the mni152. This has to be done in two steps,
1. Run mni152reg --s subject to create the anat-to-mni152 registration (needs FSL)
2. Run bbregister to get the anat-to-func reg (in lta format)
3. then combine them with mri_concatenate_lta, like
mri_concatenate_lta $SUBJECTS/subject/mri/transforms/reg.mni152.2mm.lta bbr.lta output.lta
Then use mri_vol2vol with --reg output.lta (and not --mni152reg)

On 6/15/16 5:55 AM, Leila Reddy 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