External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts,Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark
External Email - Use Caution
Great, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.czmailto:ansk@ikem.cz> wrote:
External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts,
Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
FreeSurfer has its own permutation software https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... We also have a handy interface to palm https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use Caution
Great, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.czmailto:ansk@ikem.cz> wrote:
External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts,
Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Doug,
Thanks. Unfortunately, this is only for the GLM, is there an equivalent version for the linear mixed model? I haven’t seen one. I guess we could figure out how to integrate lme into mri_glmsim, but I’m not sure that’s a better use of our time than manually running the simulations. Your thoughts?
Thanks for the help.
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:
FreeSurfer has its own permutation software https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0Perm&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844342506&sdata=%2BcICuG9wTvUlGnqpclwi21YJBtNV6YE8U2tPkr8Um6Y%3D&reserved=0 We also have a handy interface to palm https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalmhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844352500&sdata=ltksDW4GjNc%2BlSBhchWxN%2BBpn%2B0WrQbilKwkVOsW66g%3D&reserved=0
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use Caution
Great, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.czmailto:ansk@ikem.cz> wrote:
External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuidehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FPALM%2FUserGuide&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844352500&sdata=wODbvJGuGHP8dlfhO4tJjX8Ype0ph%2FbXrjMkTsGFfD8%3D&reserved=0
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts,
Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844362494&sdata=eoEproOAVUGqZFzJhjp47oUBmmjlqxOQstUL7mzs0d0%3D&reserved=0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844362494&sdata=eoEproOAVUGqZFzJhjp47oUBmmjlqxOQstUL7mzs0d0%3D&reserved=0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
I'm not sure that is a way to do this as it is quite tricky managing the exchangeability in longitudinal data. Maybe PALM can do it. I'm cc'ing Anderson in case he wants to weigh in.
On 7/28/19 7:24 PM, Mark Wagshul wrote:
External Email - Use Caution
Doug,
Thanks. Unfortunately, this is only for the GLM, is there an equivalent version for the linear mixed model? I haven’t seen one. I guess we could figure out how to integrate lme into mri_glmsim, but I’m not sure that’s a better use of our time than manually running the simulations. Your thoughts?
Thanks for the help.
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
FreeSurfer has its own permutation software *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... We also have a handy interface to palm *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use Caution
Great, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
*MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FPALM%2FUserGuide&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844352500&sdata=wODbvJGuGHP8dlfhO4tJjX8Ype0ph%2FbXrjMkTsGFfD8%3D&reserved=0
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts, Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844362494&sdata=eoEproOAVUGqZFzJhjp47oUBmmjlqxOQstUL7mzs0d0%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,
It's possible to analyse longitudinal designs with PALM. Some mild assumptions must hold, and those assumptions are different than those of an LME model. PALM doesn't assume normality, doesn't require a specified form for the dependence structure, but requires compound symmetry. PALM allows non-parametric correction of FWER and is not based on numerical optimization, so it doesn't suffer from convergence failures. On the other hand, LME allows multiple variance components and can accommodate some rather unwieldy designs, but it does make distributional and covariance assumptions and offers no trivial method (other than perhaps FDR) to deal with the multiple testing problem. It's up to you really...
All the best,
Anderson
On Mon, 29 Jul 2019 at 17:00, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I'm not sure that is a way to do this as it is quite tricky managing the exchangeability in longitudinal data. Maybe PALM can do it. I'm cc'ing Anderson in case he wants to weigh in.
On 7/28/19 7:24 PM, Mark Wagshul wrote:
External Email - Use CautionDoug,
Thanks. Unfortunately, this is only for the GLM, is there an equivalent version for the linear mixed model? I haven’t seen one. I guess we could figure out how to integrate lme into mri_glmsim, but I’m not sure that’s a better use of our time than manually running the simulations. Your thoughts?
Thanks for the help.
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
FreeSurfer has its own permutation software *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...
We also have a handy interface to palm *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use CautionGreat, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
External Email - Use CautionDear Mark,
I would suggest to use PALM instead:
*MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide <
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib....
PALM supports surface-based data. Each vertex has different area,
which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts, Hi. We are analyzing cortical thickness data in Freesurfer,
longitudinal data
in 55 subjects using the linear mixed effects package. We are
finding a number
of siginificant clusters, and would like to correct for multiple
comparisons
with permutation testing. We have already run about 2000
permutations, and
would like to use TFCE available in randomise rather than empirical
methods to
set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data
(these are F
statistics at each vertex) into a format which can be read into
randomise?
Thanks for any advice you can provide.
Best,
Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
<
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
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.
External Email - Use Caution
Anderson,
Thanks!
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.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Anderson M. Winkler Sent: Wednesday, July 31, 2019 11:10 AM Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}
External Email - Use Caution Hi,
It's possible to analyse longitudinal designs with PALM. Some mild assumptions must hold, and those assumptions are different than those of an LME model. PALM doesn't assume normality, doesn't require a specified form for the dependence structure, but requires compound symmetry. PALM allows non-parametric correction of FWER and is not based on numerical optimization, so it doesn't suffer from convergence failures. On the other hand, LME allows multiple variance components and can accommodate some rather unwieldy designs, but it does make distributional and covariance assumptions and offers no trivial method (other than perhaps FDR) to deal with the multiple testing problem. It's up to you really...
All the best,
Anderson
On Mon, 29 Jul 2019 at 17:00, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: I'm not sure that is a way to do this as it is quite tricky managing the exchangeability in longitudinal data. Maybe PALM can do it. I'm cc'ing Anderson in case he wants to weigh in.
On 7/28/19 7:24 PM, Mark Wagshul wrote:
External Email - Use CautionDoug,
Thanks. Unfortunately, this is only for the GLM, is there an equivalent version for the linear mixed model? I haven’t seen one. I guess we could figure out how to integrate lme into mri_glmsim, but I’m not sure that’s a better use of our time than manually running the simulations. Your thoughts?
Thanks for the help.
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> wrote:
FreeSurfer has its own permutation software *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.comhttp://nam02.safelinks.protection.outlook.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0Perm&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498585739&sdata=4rgKxOU39LiX8YR1kPlLMvdBzOMeRYwthXNJFLJ%2Bp0U%3D&reserved=0 We also have a handy interface to palm *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.comhttp://nam02.safelinks.protection.outlook.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalmhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498595733&sdata=iTCpthFKzmsRNX9UQS4O%2F44Yk%2BPXjWhQmeTaajixZv8%3D&reserved=0
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use CautionGreat, thanks!
Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY
Sent from my iPhone
On Jul 27, 2019, at 2:43 PM, Antonin Skoch <ansk@ikem.czmailto:ansk@ikem.cz <mailto:ansk@ikem.czmailto:ansk@ikem.cz>> wrote:
External Email - Use CautionDear Mark,
I would suggest to use PALM instead:
*MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.comhttp://nam02.safelinks.protection.outlook.com" claiming to be* https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuidehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FPALM%2FUserGuide&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498605728&sdata=uQqcMny34LpJGoDaeSaWXSNRMXivodZIniFwrhwmrEQ%3D&reserved=0 <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib....https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FPALM%2FUserGuide&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498605728&sdata=uQqcMny34LpJGoDaeSaWXSNRMXivodZIniFwrhwmrEQ%3D&reserved=0>
PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed.
Antonin Skoch
Dear Freesurfer experts, Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold.
So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise?
Thanks for any advice you can provide.
Best,
Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498615725&sdata=GdBuWWusKYFRGX8MCraJ1wIN%2F8AfLfvXq06EjFpEFeA%3D&reserved=0 <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498615725&sdata=GdBuWWusKYFRGX8MCraJ1wIN%2F8AfLfvXq06EjFpEFeA%3D&reserved=0>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "nam02.safelinks.protection.outlook.comhttp://nam02.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498625722&sdata=O5pyY3mTTY773OJa6r1LapuE1iVBcpxygW43Uf9KmXc%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498625722&sdata=O5pyY3mTTY773OJa6r1LapuE1iVBcpxygW43Uf9KmXc%3D&reserved=0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498635723&sdata=6jyy%2Bvhg0mjj%2F%2F0iqSc9C%2FCRTggbp4p4F4ZzZW40Sm8%3D&reserved=0
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/compliancelinehttps://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498645709&sdata=6GIZK8XGtHc4X7r%2FaLKEJCcXIJEGQN3CbnhXJ642n1w%3D&reserved=0 . 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.
freesurfer@nmr.mgh.harvard.edu
-
Anderson M. Winkler -
Antonin Skoch -
Greve, Douglas N.,Ph.D. -
Mark Wagshul