You can also convert, eg, thickness, to mgz
mri_convert lh.thickness lh.thickness.mgz
Then load the mgz in matlab, eg,
th = MRIread('lh.thickness.mgz');
then replace the pixel data with your own
th.vol = YourData;
Then write out the result
MRIwrite(th,'lh.yourdata.mgz');

On 5/19/2019 5:26 PM, Bruce Fischl wrote:

Hi Amanda

for a surface overlay M is irrelevant (it is a vox2ras or ras2vox matrix, can't remember what). Just give it eye(4). If you are in fsaverage coords I believe it is already in MNI space. If you want to convert to a volume you can use mri_surf2vol

cheers
Bruce
On Sun, 19 May 2019, Worker, Amanda wrote:

External Email - Use Caution

Hi,

I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to
firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to
MNI space and write it out as a volume (preferably nifti).

I think that save_mgh might be what I need but I don't understand what M is and how I would get that
info for a statistical map in fsaverage space. Any ideas would be much appreciated.

Thanks in advance,

Amanda
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