Re: [Freesurfer] Cortical Thickness Zero Values

[Douglas Greve]

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 
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
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 


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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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Re: [Freesurfer] Cortical Thickness Zero Values

[Bruce Fischl]

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  
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 

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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The information in this e-mail is intended only for the person to 
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the e-mail
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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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Re: [Freesurfer] Cortical Thickness Zero Values

[Taha Abdullah]

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 
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
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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
>> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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
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> 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*
___
Freesurfe

Re: [Freesurfer] Cortical Thickness Zero Values

[Bruce Fischl]

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  
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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contains patient information, please contact the Partners Compliance HelpLine at
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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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Re: [Freesurfer] Cortical Thickness Zero Values

[Taha Abdullah]

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 
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 <%28312%29-451-8468>*
>
>
> ___
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>
>
>
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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
> 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*
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Re: [Freesurfer] Cortical Thickness Zero Values

[Douglas Greve]

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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[Freesurfer] Cortical Thickness Zero Values

[Taha Abdullah]

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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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
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