You can break the aparc.annot into individual labels with mri_annotation2label, then merge the labels of each lobe into a single lobe label with mri_mergelabels, then combine the lobe labels into an annotation with mris_label2annot. The 3rd link below is probably the most useful one for this.

doug

Allison Stevens wrote:

Mustafa, There are a couple of relevant pages with information on this. These: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13908.html

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04901.html Allison

tksurfer subject lh inflated -annot yourfile.annot

Don't know anything about #2.

doug

Mustafa, Nazahah wrote:

Hi ...

Thank you for the replies.

Now we already have an individual label of frontal, occipital, parietal and temporal lobes and their annot files (after converting using mris_label2annot). At this moment, we want to visualise these lobes as 3D image.

1. Can we do that using this annot files and how?

2. Is it possible to visualize the £D image using imageJ/mricron?

Your response is highly appreciated.

Thank you

Regards; Naza

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 06 October 2010 18:14 To: Allison Stevens Cc: Mustafa, Nazahah; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Marking four majors lobes: frontal, parietal, temporal, occipital

You can break the aparc.annot into individual labels with mri_annotation2label, then merge the labels of each lobe into a single lobe label with mri_mergelabels, then combine the lobe labels into an annotation with mris_label2annot. The 3rd link below is probably the most useful one for this.

doug

Allison Stevens wrote:

...

Mustafa, There are a couple of relevant pages with information on this. These: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13908.html

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04901.html Allison

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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