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
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
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
Hi Esther
I don't see a volume overlay, just one on the inflated surface. Is that what you mean? If not, can you resend and explain?
Bruce
On Thu, 2 Jun 2011, Esther Walton wrote:
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
Hi Bruce,
Yes, I mean the one on the inflated surface. I found this view easier to judge how well the label and the nii.gz match. Is that a problem?
Thanks, Esther
Date: Thu, 2 Jun 2011 08:36:27 -0400 From: fischl@nmr.mgh.harvard.edu To: estherkillat@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label
Hi Esther
I don't see a volume overlay, just one on the inflated surface. Is that what you mean? If not, can you resend and explain?
Bruce
On Thu, 2 Jun 2011, Esther Walton wrote:
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
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