On 8 May 2013 16:54, Douglas N Greve <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
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Fax: 617-726-7422

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