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 this<http://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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
