Re: [Freesurfer] Labels and parcellations

On 05/08/2013 12:02 PM, Tudor Popescu wrote:

Thanks Doug. Follow-ups below

2. ..and when would you use a surface mask versus a surface label?

It is just a matter of convenience.

3. (it seems you skipped over this one:) )

Sorry:) what are you going to do with the ROI?

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

On 8 May 2013 16:54, Douglas N Greve <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
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