For #1, do the parcellations look ok? Do the surfaces look ok in the volume?
On 10/20/16 4:09 PM, Taha Abdullah wrote:
Hi Dr. Fischl and Dr. Greve,
#1 So moving the mouse over the medial wall seems to have all vertices
within that to have a zero mm thickness as expected. The yellow
outline is the lh.cortex.label and it seems to look good to me i.e.
majority of the medial wall is properly masked. To be noted, this was
the subject with 53 vertices labeled as 0s, which as you mentioned
should be a substantial number. I am wondering what could be causing
this?
#2 Lastly, I was wondering for cortical thickness analysis, is there a
method to ensure the same number of vertices across all subjects with
a corresponding mm thickness value. I have yet to try some commands,
but preemptively I think if using mri_label2label with the
trglabel lh.cortex.label as found in fsaverage directory and for each
subject map their lh.cortex.label to fsaverage's lh.cortex.label and
then from here I know I can run mris_anatomical_stats to extract
average thickness, is there a command maybe using mris_convert with
the label option to convert the label to the white surface and then
using mris_convert with a -c option to have the scalar mm values
corresponding to each vertex? or is this not a recommended approach? I
would like ultimately import this into MATLAB to do some statistics
and then view in freeview as a scalar overlay. Please advise.
Thanks for the help,
Taha
On Tue, Oct 18, 2016 at 7:49 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Taha
none that I can think of. The medial wall is pretty substantial
region though - I am more concerned about your subject with only
53 vertices in it. You can visualize it by loading the
?h.cortex.label onto the inflated surface. Everything not in the
label should be set to 0
cheers
Bruce
On Tue, 18 Oct 2016, Taha Abdullah wrote:
I see now, thanks for the answer. If I may, is there any
particular reason why such a disparity between
two subjects, is this due to anatomical variability between
individuals? I was surprised by the 9,000
values that was missing.
On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
The entire medial wall has thickness values of 0 because
there is no cortex there. There
needs to be a surface in that area because we need a
closed surface.
On 10/12/16 8:10 PM, Taha Abdullah wrote:
Hello All,
Quick question, I ran recon-all with the qcache option and
after converting the
?.thickness.fsaverage.mgh to an ascii text file via
mri_convert I am noticing some vertices
have 0mm thickness and it varies, for example, one subject had
53 vertices labeled as zeros
while another had over 9,000 vertices. Is there a method I can
use to have a thickness value
for each of the 163000+ vertices? I am not sure if this is a
possible registration issue to
mni305.
Thanks in advance,
Taha
--
Taha Abdullah
Department of Physiology,
Northwestern University Feinberg School of Medicine
MS in Physiology and Biophysics, Georgetown University 2015
Work Cell: (312)-451-8468 <tel:%28312%29-451-8468>
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Taha Abdullah
Department of Physiology,
Northwestern University Feinberg School of Medicine
MS in Physiology and Biophysics, Georgetown University 2015
Work Cell: (312)-451-8468 <tel:%28312%29-451-8468>
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/Department of Physiology,/
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/
/MS in Physiology and Biophysics, Georgetown University 2015/
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