I guess you could compute the intersection of the cortex labels. Easy
enough to do in matlab once you map them all to a common space. Not sure if
we have anything that will do it, but we might. Perhaps someone else knows?
cheers
Bruce
cheers
Bruce
On Thu, 20 Oct
2016, Taha Abdullah wrote:
Hi Dr. Fischl and Dr. Greve,
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?
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>
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>
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
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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
_______________________________________________
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
--
Taha Abdullah
Department of Physiology,
Northwestern University Feinberg School of Medicine
MS in Physiology and Biophysics, Georgetown University 2015
Work Cell: (312)-451-8468
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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