Hello,
I have two questions:
First: I made left hemisphere anatomical ROIs using the freesurfer cortical parcellation atlas and fsaverage's data. However, when I convert these ROIs from .mgz to an SPM-compatible format (.img), the LH ROIs show up on the right. Any idea on how to resolve this problem?
The ROIs I need are customized (i.e., I needed to merge some of the areas, and did so via relabeling), but for simpler purposes let's just say I used lh.BA44.label for now. Here are the commands I used:
cd $FREESURFER_HOME/subjects/fsaverage mri_label2vol --label label/lh.BA44.label --temp mri/T1.mgz --identity --o lh.BA44.mgz mri_convert lh.BA44.mgz lh.BA44.img
Second: I would like to normalize these anatomical ROIs to MNI space in SPM. To do this I was thinking about taking fsaverage's anatomical file, converting it to an SPM-compatible format, estimate the normalization parameters from fsaverage's anatomical to SPM's T1 template, and then writing those parameters to the anatomical ROIs. Therefore am I correct in converting fsaverage's T1.mgz to .img since I am specifying that as the template in the mri_label2vol above?
Thanks!