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 <greve@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> 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> 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
        <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu

        <mailto: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.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
            >
            >
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