There’s 2 options:

1. Merge the 1mm segmentations (i.e., the *.FSvoxelSpace.mgz). This is easy as they live in the same voxel space, you can directly sum the images. The problem is that they have less resolution.

2. Merge at higher resolution. This will create HUGE volumes. You could try something like:

mri_convert nu.mgz dummy.mgz --voxsize 0.3333333 0.3333333 0.3333333

mri_convert lh.hippoAmygLabels-T1.v21.mgz lh.highres.mgz -rl dummy.mgz -rt nearest

mri_convert rh.hippoAmygLabels-T1.v21.mgz rh.highres.mgz -rl dummy.mgz -rt nearest

and then combine lh.highres.mgz and rh.highres.mgz.

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Jul 19, 2021, at 11:08, Gregorio Borghi <gregorio.borghi.uk@gmail.com> wrote:

External Email - Use Caution

Dear sir/madam,

After the segmentation I obtained the hippocampal segmented file for each hemisphere. Since I want to use them as mask for my functional scans, I wanted to join the the 2 hemisphere files together (otherwise I would obtain a different Multiple comparison computation), but when i tried doing that in FSL (fslmaths) the 2 files were joined but in very different spatial configuration. Is there a way to join the 2 hemisphere file in Freesurfer?

--

Kind regards,
Gregorio

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