Sorry, one more iteration: 1) Command "mri_annotation2label --subject 01 --hemi lh --aparc.a2009s --outdir $SUBJECTS_DIR/01/myLabelsDestrieux" doesn't recognise the aparc.2009s flag (I tried a few other variations with no luck)!
1') Assuming the above command works and I get .label files corresponding to all Destrieux structures, what is the exact call to mri_glmfit that will do the two contrasts I mentioned (group comparison of CT, and comparison of CT-behaviour correlation)? 1'') How should the design matrix & contrast files (arguments for calling mri_glmfit) be created, for these analyses? 2) ..so when would I use a mask, in a ROI analysis, as opposed to a label? 3) I'm still not sure as to the answer to my question: regardless of what space I do it in, does it pay off to create the label/mask that I"ll use in the ROI analysis *manually *for each individual subject (i.e. taking into account individual anatomy), as opposed to just taking it from an atlas and using *the same *label/mask with *all *subjects? 4) Bingo - this creates an image as I wanted, but now the mouse cursor no longer tells me the structure above which I hover the mouse (so a legend to each color, much like in Fig 1 of the Desikan paper) I really appreciate your patience Doug, thanks :) Tudor On 8 May 2013 18:56, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > On 05/08/2013 01:28 PM, Tudor Popescu wrote: > >> >> 2) ..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.. >> > A label is a text file with a list of points in the label. A mask is > binary file (eg, mgh or nii) with 1s where the mask is and 0s otherwise. > > >> 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 >> > If you're doing the final analysis in the group space, then just use the > ROI in the group space. > >> >> 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) >> >> that was generated with tksurfer, something like tksurfer subject >> lh pial -aparc >> >> Using that command, I get a brain <http://www.4shared.com/photo/** >> sRcnX93M/8-05-2013_18-25-04.**html<http://www.4shared.com/photo/sRcnX93M/8-05-2013_18-25-04.html>> >> that has only little of its surface coloured, unlike the image < >> http://brainybehavior.com/**neuroimaging/wp-content/** >> uploads/2010/05/jt_rh_pial_**freesurfer_tksurfer.png<http://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pial_freesurfer_tksurfer.png>> >> that 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) >> > Change the annotation mode to be filled instead of outline mode. In the > tksurfer control window, it is the 4th button from the right on the top > row. It will say "Draw Filled Labels" when you put the mouse over it > >> >> >> >> On 8 May 2013 16:54, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <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<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 >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@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 >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@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> >> > >> >> <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> >> > >> <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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@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 >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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/> >> >> >> > -- > 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<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> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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