Hi FS Experts,

I'm trying to use the mni152reg command but I get an error that --lta is not recognized.

It appears that fslregister doesn't have this option. There was a previous post about this problem

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html

but I can't figure out if the problem had been solved. The version of mni152reg I am using is

$Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8.

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