Thanks Doug. Follow-ups below 2) ..and when would you use a surface mask versus a surface label?
3) (it seems you skipped over this one:) ) 4) This opens up a coronal slice rather than a 3D image as in the picture I linked to. Do I need to do anything else in tkmedit after it opens? (I tried pressing some buttons, and some menu options, with no luck) On 8 May 2013 16:54, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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. > >
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