Thanks Doug. Follow-ups below
2) ..and when would you use a surface mask versus a surface label?
3) (it seems you skipped over this one:) )
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)
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!!
- 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
- 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.
- 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?
- 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...
, 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
- 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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