I looked at your data. The problem is that the T2-pial placement is not very good.  In some places it is much thinner, in some places it it somewhat thicker. This makes the volume computation a little unpredictable (can't just assume that average thickenss*area will give  you a reasonable value). The T2-pial is not placed well because the T2 is very low resolution (3mm slice thickness); it is hard to determine the boundaries of a 2-3mm structure when your slices are 3mm


On 11/10/2021 10:55 AM, Castro Leal, Gonzalo wrote:

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I have tried, but I get the following error:

local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: Gonzalo_ADNI_sub-020S0899_T2.tar.gz
421 Service not available, remote server has closed connection


De: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve@mgh.harvard.edu>
Enviado: miércoles, 10 de noviembre de 2021 15:09
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
 
Ah, I see. Can you upload those two subjects using the method below?

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:

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Sorry I did not explain myself well. For some regions of the brain this is what happens:

Region                                                                         Num Vertices   Surf Area    GrayVol   ThickAvg
lateralorbitofrontal                     2969   2085   5489  2.469
lateralorbitofrontal                     2969   2085   5173  2.566
The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.  

PD: the last mail was sent by mistake, sorry for the spam.

Many thanks,
Gonzalo.
De: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve@mgh.harvard.edu>
Enviado: martes, 9 de noviembre de 2021 20:13
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
 
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?

On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:

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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else?
De: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve@mgh.harvard.edu>
Enviado: martes, 9 de noviembre de 2021 18:09
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
 
Were the stats files regenerated? Check the modification date

On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:

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Yes the pial surface changed and the white did not. 
De: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Enviado: martes, 9 de noviembre de 2021 14:49
Para: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
 

⚠ Caution: External sender


The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?

On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:

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Hello,

I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change?
(I used freesrufer 7.1.1)


Many thanks,
Gonzalo.

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