Re: [Freesurfer] Labels and parcellations

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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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