Hi Jenny 1) yes, they are usually fine, but you *always* should look at the regions you are hoping to make biological statements about.

2) mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.nii

Wold convert the aseg. Not that they are already in the original RAS space, just a different voxel space Cheers Bruce

On Dec 20, 2012, at 6:48 AM, Jenny Mercolini jennymercolini@gmail.com wrote:

Hi Freesurfers,

I am new to this software and i am trying to learn how to use it.

I have two questions:

1. if I do recon-all on a group of 20 subject, and I am primarily interested in a few regions (In my case - amygdala, insula and anterior cingulate cortex), do I have to edit all the datasets in tkmedit to make sure that these ROIs are "where they ar supposed to be"?

2. What is the easiest way to convert recon'ed data from FreeSurfer space to original subject space ( and mgz files to nifti files)?

Thank you so much for your help!

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