Thanks so much for your input.

Could somebody please answer the second part of the question?
That is, ignoring the fact that the label looks a bit weird as it is, is the overlay between the label and the volume okay, as seen in the second file I attached in my first email? If not, any idea what could have gone wrong?

Thanks for all your help,

Esther

Date: Tue, 31 May 2011 10:36:06 +0200
From: christophe.destrieux@univ-tours.fr
To: estherkillat@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

Hi Esther

I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus is indeed weird.

Why don't you use the 2009 version of the atlas that includes major improvements ; this parcellation is fully described in

Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. ; Destrieux C, Fischl B, Dale A, Halgren E. ; Neuroimage. 2010 Oct 15;53(1):1-15

I let Bruce or Doug answer the second part of your question ; cheers

PS I attached a snapshot of the 2009 parcellation for the same hemi

--
Christophe Destrieux,

Directeur du Département Communication et Multimedia
http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612

Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université François Rabelais de Tours
http://www.u930.tours.inserm.fr/

Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - France
tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07


De: "Esther Walton" <estherkillat@hotmail.com>
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 30 Mai 2011 23:41:24
Objet: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

Dear list,
 
I am interested in the S_intraparietal-and_Parietal_transverse label from
the Desitreux atlas using aparc.a2005s.annot.
 
If I load this into fsaverage, it has three regions to it (see dark purple
label in the attached screenshot): two big ones, very close to each other,
connected by two narrow bridges, and another much smaller region more
dorsally.
 
Does this look fine to you?!
 
Secondly, assuming this is ok, I created labels for each subject using
mri_annotation2label and turned those labels into ROIs in standard space
using
 
mri_label2vol --label
xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp
xx/reg_standard/example_func.nii.gz --reg
xx/reg/freesurfer/anat2std.register.dat --o
xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz
 
However, when I load this volume with:
 
tksurfer fsaverage lh inflated -overlay
lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1
-fmax 1
 
it looks a bit off (see yellow label and red ROI in second screenshot).
 
Would you think that's still ok taking into account the individual anatomy
or did something go wrong somewhere?
 
Thanks for your help,
 
Esther

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