External Email - Use Caution
Of course!
To do GLM for volume and surface area analysis, is there any change in commands in relation to cortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
Many thanks!
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On 3/09/2022 15:20 PM, Douglas N. Greve wrote:
Can you just ask the question again so I don't have to sort it out myself?
---------------------------------------------------------------------------------------
On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:
Thanks so much for the explanation!
There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
------------------------------------------------------------------------------
On 2/21/2022 15:20 PM, Douglas N. Greve wrote:
Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring truncated tetrahedra. When you run mris_preproc, it will apply a jacobian correction (like VBM). Otherwise, it operates the same as if you had a thickness value at the vertex, ie, same GLM, etc. Make sure to use permutation for correction of multiple comparisons.
-----------------------------------------------------------------------------------------
On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:
Hello FreeSurfer Developers,
I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!?
In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!?
I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me?
Thanks in advance!
Att, Laura Willers de Souza
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
Hi, sorry for the late response. No, there is nothing else you have to do. Using perm is a really good idea with volume and area, so glad to hear that is what you are doing. best doug
On 3/10/2022 8:21 AM, Laura Willers de Souza wrote:
External Email - Use Caution
Of course!
To do GLM for volume and surface area analysis, is there any change in commands in relation tocortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
Many thanks!
On 3/09/2022 15:20 PM, Douglas N. Greve wrote:
Can you just ask the question again so I don't have to sort it out myself?
On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:
Thanks so much for the explanation!
There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
On 2/21/2022 15:20 PM, Douglas N. Greve wrote:
Yes, it is. It is confusing when you talk about area and volume sincethese are not point measures like thickness (ie, what is the volume orarea of a vertex?). The area of a vertex is computed as the mean of theadjacent triangles of the vertex. The volume is the mean of theneighboring truncated tetrahedra. When you run mris_preproc, it willapply a jacobian correction (like VBM). Otherwise, it operates the sameas if you had a thickness value at the vertex, ie, same GLM, etc. Makesure to use permutation for correction of multiple comparisons.
On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:
Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surfacearea analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions forperforming these types of analysis. But I understand that freesurferdoes vertex-wise analysis in the 2D surface space. So, it is not clearto me how it is possible to evaluate a 3D measurement, as volume, witha 2D method!? I've also read that surface area analysis via vertex-wise analysisdoesn't make much sense. The best would be to do ROI-based analysis.Can you explain that to me? Thanks in advance!Att,
*Laura Willers de Souza *
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
External Email - Use Caution
Ok! Thanks so much for the answer!
Best, Laura. ________________________________ De: Douglas N. Greve dgreve@mgh.harvard.edu Enviado: segunda-feira, 28 de março de 2022 00:29 Para: Laura Willers de Souza laura.w.desouza@hotmail.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] GLM analysis - volume and surface area
Hi, sorry for the late response. No, there is nothing else you have to do. Using perm is a really good idea with volume and area, so glad to hear that is what you are doing. best doug
On 3/10/2022 8:21 AM, Laura Willers de Souza wrote:
External Email - Use Caution
Of course!
To do GLM for volume and surface area analysis, is there any change in commands in relation to cortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
Many thanks!
------------------------------------------------------------------------------
On 3/09/2022 15:20 PM, Douglas N. Greve wrote:
Can you just ask the question again so I don't have to sort it out myself?
---------------------------------------------------------------------------------------
On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:
Thanks so much for the explanation!
There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons.
------------------------------------------------------------------------------
On 2/21/2022 15:20 PM, Douglas N. Greve wrote:
Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring truncated tetrahedra. When you run mris_preproc, it will apply a jacobian correction (like VBM). Otherwise, it operates the same as if you had a thickness value at the vertex, ie, same GLM, etc. Make sure to use permutation for correction of multiple comparisons.
-----------------------------------------------------------------------------------------
On 2/21/2022 12:13 PM, Laura Willers de Souza wrote:
Hello FreeSurfer Developers,
I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!?
In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!?
I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me?
Thanks in advance!
Att,
Laura Willers de Souza
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
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