Hello all,
I have some more burning questions, for which I thank you in advance!!
1) I expected that "mri_annotation2label --subject 01 --hemi lh --outdir $SUBJECTS_DIR/myLabels" would give me labels corresponding to structures of the standard FreeSurfer atlas (Destrieux), instead it produced labels with completely different names, e.g. "lh.postcentral.label" instead of the Destrieux name "lh_S_postcentral". Exactly how different are they, and which ones should be used in mri_glmfit for ROI analyses?
2) Does it make sense to use mri_glmfit with volumetric masks, or should it only be used with labels?
3) Say I want to do a ROI analysis for a particular brain structure; how much is there to gain by manually (visually) creating a label/mask for that structure in each subject (i.e. taking into account individual anatomy), as opposed to just using an atlas to create a single label/mask for use with all subjects?
4) I used the command "tkmedit 01 aparc+aseg.mgz" (I also tried adding " -aux brainmask.mgz -surfs –aseg"), thinking that it would display an image like thishttp://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pial_freesurfer_tksurfer.png, i.e. with all the main cortical structures displayed in different colours. Does aparc+aseg.mgz not contain all the necessary information to produce such an image?
5) Which mask file corresponds to the brain extraction procedure of recon-all? I see that a subject's /mri/brainmask.mgz is not a binary map, as expectd, but instead a BETted (skull-stripped) version of that subject's structural.
Thank you so much for your help! Tudor