Hello all,<br><br>I have some more burning questions, for which I thank you in advance!!<br><br>1) I expected that &quot;mri_annotation2label --subject 01 --hemi lh --outdir $SUBJECTS_DIR/myLabels&quot; would give me labels corresponding to structures of the standard FreeSurfer atlas (Destrieux), instead it produced labels with completely different names, e.g. &quot;lh.postcentral.label&quot; instead of the Destrieux name &quot;lh_S_postcentral&quot;. Exactly how different are they, and which ones should be used in mri_glmfit for ROI analyses?<br>

<br>2) Does it make sense to use mri_glmfit with volumetric masks, or should it only be used with labels?<br><br>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?<br>

<br>4) I used the command &quot;tkmedit 01 aparc+aseg.mgz&quot; (I also tried adding &quot; -aux brainmask.mgz -surfs –aseg&quot;), thinking that it would display an image like <a href="http://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pial_freesurfer_tksurfer.png">this</a>, 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?<br>

<br>5) Which mask file corresponds to the brain extraction procedure of 
recon-all? I see that a subject&#39;s /mri/brainmask.mgz is not a binary map, as expectd,
 but instead a BETted (skull-stripped) version of that subject&#39;s 
structural.<br><br>Thank you so much for your help!<br>Tudor<br>