Almost. You'll need to run mri_annotation2label to extract the individual labels from the annot, then use mri_mergelabels to merge the ones you want.

doug

Jenni Pacheco wrote:

I think that mri_mergelabels will do all the steps that Rahul describes below for you. You can input as many labels as you want (i think) and specify an output name.

USAGE: mri_mergelabels

-i label1 -i label2 ... -o outputlabel

good luck, Jenni

On Thu, 27 Jul 2006, Rahul Desikan wrote:

...

Hi Dhruman,

To the best of my knowldge, the wiki page does not contain any information on using tksurfer to add labels together. My suggestion would be the following:

1. Load the subject in using tksurfer (tksurfer subjectname hemi

inflated)

2. Load in the parcellation you want to edit (e.g. rh.aparc.annot)

3. Click on a label of interest to you (e.g. caudalmiddlefrontal)

4. Then, click the 'Custom Fill' button in the Tksurfer Tools window.

This button looks like a paint can and can be found in the second row of the Tksurfer Tools window. Keep this 'Custom Fill' window open for later (see steps 5-8 below).

5. Choose only the 'Up to other labels' option in the 'Custom Fill'

options bar

6. In the tksurfer window where you can see the rh.aparc.annot file

loaded and the inflated surface, click on a label you would like to add (e.g. rostralmiddlefrontal).

7. Then go to the 'Action' portion of the 'Custom Fill' options bar

and choose 'Add to existing label'. If you look at the label bar below, it should show you which label you are adding to.

8. Repeat steps 6 and 7 for all labels you would like to add to the

original one you have already selected (e.g. add rostralmiddlefrontal, superiorfrontal, precentral, parsopercularis, etc.-->to caudalmiddlefrontal, the label you had already selected).

9. Once you have selected all the labels you would like to have added

together, click the new label, make sure it is highlighted and save it as a new label (e.g. rh.frontal.label)

I am including an image that shows what the final result might look like for the frontal lobe (lateral view) once you have added together all of your frontal subregions together.

best,

Rahul

On Thu, 27 Jul 2006, Goradia, Dhruman D wrote:

...

Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label

Hi Dhruman,

If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that

lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine:

lateral occipital cuneus lingual pericalcarine

and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated.

best,

Rahul

On Thu, 27 Jul 2006, Goradia, Dhruman D wrote:

...

Hi all,

I am interested in lobe wise surface measurement. I read Desikan et

al.

...

paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse

all

...

the region belonging to each lobe and create a new label, which I

could

...

use to get surface measurement? Thanks in advance.

Dhruman

---

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