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Dear FreeSurfer users/experts,
I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable "Zcols"). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the "patch" function with the results projected onto lhsphere.
We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide.
Best,
Mark
____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
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Yes,
that's possible due to the vertex correspondence between e.g. 'lh.shere' and 'lh.inflated'.
You could import the 'lh.inflated' file from the fsaverage directory in a similar manner as the 'lh.sphere' file.
A caveat may be that, if I am understanding your procedure correctly, the covariance matrices are just 'intermediate results', and significance cannot not be inferred from these maps.
The very last section of the tutorial on the LME webpage has an example how to export signifiance from Matlab so that they can be displayed in Freeview, but this requires that the whole LME procedure including covariance estimation, modeling fitting, inference has been run through.
Hope this helps,
Kersten
On Mi, 2019-06-19 at 15:56 +0000, Mark Wagshul wrote:
External Email - Use Caution Dear FreeSurfer users/experts,
I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable “Zcols”). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the “patch” function with the results projected onto lhsphere.
We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide.
Best,
Mark
____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
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External Email - Use Caution
Thanks. Yes, we understand that, and now have the model significance maps to look at. But, just to be clear: once we have exported the significance (or beta) maps using fs_write_Y, we should be able to open up this object as a surface, correct? Our first attempt at this failed, saying that this was not a valid surface. Any advice would be most welcome.
Best,
Mark
P.S. I see that you responded to a similar question from my student Daliah, so no need to continue that thread. ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Diers, Kersten /DZNE Sent: Wednesday, June 26, 2019 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer linear mixed models - viewing results
External Email - Use Caution Yes,
that's possible due to the vertex correspondence between e.g. 'lh.shere' and 'lh.inflated'.
You could import the 'lh.inflated' file from the fsaverage directory in a similar manner as the 'lh.sphere' file.
A caveat may be that, if I am understanding your procedure correctly, the covariance matrices are just 'intermediate results', and significance cannot not be inferred from these maps.
The very last section of the tutorial on the LME webpage has an example how to export signifiance from Matlab so that they can be displayed in Freeview, but this requires that the whole LME procedure including covariance estimation, modeling fitting, inference has been run through.
Hope this helps,
Kersten
On Mi, 2019-06-19 at 15:56 +0000, Mark Wagshul wrote:
External Email - Use Caution Dear FreeSurfer users/experts,
I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable “Zcols”). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the “patch” function with the results projected onto lhsphere.
We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide.
Best,
Mark
____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
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Hi,
the files that are generated with fs_write_Y are not surfaces per se, but rather surface overlays.
At first, one has to load the (e.g.) lh.inflated or rh.inflated surface (typically from the fsaverage directory).
Then, the generated files can be overlaid using 'overlay' --> 'load generic' within the GUI.
Best regards,
Kersten
On Fr, 2019-06-28 at 15:50 +0000, Mark Wagshul wrote:
External Email - Use Caution Thanks. Yes, we understand that, and now have the model significance maps to look at. But, just to be clear: once we have exported the significance (or beta) maps using fs_write_Y, we should be able to open up this object as a surface, correct? Our first attempt at this failed, saying that this was not a valid surface. Any advice would be most welcome.
Best,
Mark
P.S. I see that you responded to a similar question from my student Daliah, so no need to continue that thread. ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Diers, Kersten /DZNE Sent: Wednesday, June 26, 2019 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer linear mixed models - viewing results
External Email - Use Caution Yes,
that's possible due to the vertex correspondence between e.g. 'lh.shere' and 'lh.inflated'.
You could import the 'lh.inflated' file from the fsaverage directory in a similar manner as the 'lh.sphere' file.
A caveat may be that, if I am understanding your procedure correctly, the covariance matrices are just 'intermediate results', and significance cannot not be inferred from these maps.
The very last section of the tutorial on the LME webpage has an example how to export signifiance from Matlab so that they can be displayed in Freeview, but this requires that the whole LME procedure including covariance estimation, modeling fitting, inference has been run through.
Hope this helps,
Kersten
On Mi, 2019-06-19 at 15:56 +0000, Mark Wagshul wrote:
External Email - Use Caution Dear FreeSurfer users/experts,
I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable “Zcols”). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the “patch” function with the results projected onto lhsphere.
We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide.
Best,
Mark
____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461
Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul@einstein.yu.edumailto:mark.wagshul@einstein.yu.edu
[einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
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Mark Wagshul