Hi,
I have two questions:
1. I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them.
2. How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere?
Can anybody provide the appropriate commands for both issues?
Thank you very much!
Best wishes, Robert
-- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch)
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Hi Robert, On 06/03/2013 12:12 PM, Robert Schulz wrote:
Hi, I have two questions:
I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them.
I don't understand what you mean. What are you thresholding? The thickness?
How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere?
You can run mri_glmfit with a --mask option to select only the voxels you want to use doug
Can anybody provide the appropriate commands for both issues? Thank you very much! Best wishes, Robert
-- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch)
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Dear Douglas,
thank you for your reply.
Hi, I have two questions:
I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them.
I don't understand what you mean. What are you thresholding? The thickness?
No, to make it clear. Surfaces will include data derived from FSL fiber tracking to investigate the structural connectivity of this specific surface ("brain area"). So the actual surface is just a binary (1) "mask". I'd like to know the common "core" surface hence the surface common to all 20 subjects. How can I calculate this final surface whose area can be found in all 20 subjects. It's just about the localization of the surface. It's about where this surface is located in all subjects. I just thought to add all surfaces with their 1s in ther vertices and see where I get 20. I hope this makes it clearer.
How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere?
You can run mri_glmfit with a --mask option to select only the voxels you want to use
mri_glmfit will be conducted based on the surface. so as --mask, I can use the finalmask.mhg?
Thank you!
doug
Can anybody provide the appropriate commands for both issues? Thank you very much! Best wishes, Robert
-- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch)
Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt zuliebe.
Please consider whether this mail must be printed - please think of the environment.
On 06/03/2013 12:37 PM, Robert Schulz wrote:
Dear Douglas,
thank you for your reply.
Hi, I have two questions:
I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them.
I don't understand what you mean. What are you thresholding? The thickness?
No, to make it clear. Surfaces will include data derived from FSL fiber tracking to investigate the structural connectivity of this specific surface ("brain area"). So the actual surface is just a binary (1) "mask". I'd like to know the common "core" surface hence the surface common to all 20 subjects. How can I calculate this final surface whose area can be found in all 20 subjects. It's just about the localization of the surface. It's about where this surface is located in all subjects. I just thought to add all surfaces with their 1s in ther vertices and see where I get 20. I hope this makes it clearer.
You can use mri_concat xy.subj1.mgh xy.subj2.mgh ... --sum --o sum.mgh mri_binarize --i sum.mgh --min 19.5 --o mask.mgh then run mri_glmfit with --mask mask.mgh
doug
How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere?
You can run mri_glmfit with a --mask option to select only the voxels you want to use
mri_glmfit will be conducted based on the surface. so as --mask, I can use the finalmask.mhg?
Thank you!
doug
Can anybody provide the appropriate commands for both issues? Thank you very much! Best wishes, Robert
-- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch)
Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt zuliebe.
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freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Robert Schulz