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