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:[EMAIL PROTECTED]
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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