On 05/08/2013 11:43 AM, Tudor Popescu wrote: > 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? That is the Desikan/Killiany atlas it uses by default. Tell it to use aparc.a2009s to get Destrieux > > 2) Does it make sense to use mri_glmfit with volumetric masks, or > should it only be used with labels? If you are analyzing surface data you have to give it a surface mask or a surface label. > > 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? try tkmedit subject orig.mgz -seg aparc+aseg.mgz > > 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. We don't create a binary mask. You can with mri_binarize --i brainmask.mgz --min 0.5 --o binarymask.mgz
doug > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
