- ..and when would you use a surface mask versus a surface label?
It is just a matter of convenience.
Sorry, I meant I don't really understand what the difference is between a label and a mask, and in which circumstances each should be used. I tried finding an answer on the wiki but no luck..
3) (it seems you skipped over this one:) )
Sorry:) what are you going to do with the ROI?
Use it mri_glmfit, in order to compare cortical thickness in that ROI between groups, and also (in a different design) to compare the correlations between thickness and a behavioural predictor
- 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)
that was generated with tksurfer, something like tksurfer subject lh pial -aparc
Using that command, I get a brainhttp://www.4shared.com/photo/sRcnX93M/8-05-2013_18-25-04.htmlthat has only little of its surface coloured, unlike the imagehttp://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pial_freesurfer_tksurfer.pngthat I linked to, in which it seems each major structure is identified in its own colour, and these colours fill up the entire brain (there's no grey surface left)
On 8 May 2013 16:54, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@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.pnghttp://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 <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/