Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed} {Disarmed}

2019-08-01 Thread Mark Wagshul 
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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
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From: freesurfer-boun...@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. 
mailto:dgr...@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 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.
> mailto:dgr...@mgh.harvard.edu> 
> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>> wrote:
>
>> FreeSurfer has its own permutation software
>> *MailScanner has detected a possible fraud attempt from
>> "nam02.safelinks.protection.outlook.com<http://nam02.safelinks.protection.outlook.com>"
>>  claiming to be*
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FMultipleComparisonsV6.0Perm=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498585739=4rgKxOU39LiX8YR1kPlLMvdBzOMeRYwthXNJFLJ%2Bp0U%3D=0>
>> We also have a handy interface to palm
>> *MailScanner has detected a possible fraud attempt from
>> "nam02.safelinks.protection.outlook.com<http://nam02.safelinks.protection.outlook.com>"
>>  claiming to be*
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7C68cba67d55464e681f6f08d715c944c8%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637001826498595733=iTCpthFKzmsRNX9UQS4O%2F44Yk%2BPXjWhQmeTaajixZv8%3D=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 
>>> mailto:a...@ikem.cz>
>>> <mailto:a...@ikem.cz<mailto:a...@ikem.cz>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Dear Mark,
&

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}

2019-07-31 Thread Anderson M. Winkler 
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. <
dgr...@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 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.
> > mailto:dgr...@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/MultipleComparisonsV6.0Perm
> >> 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  >>> > 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=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844352500=wODbvJGuGHP8dlfhO4tJjX8Ype0ph%2FbXrjMkTsGFfD8%3D=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  >
> 
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Cb7ea74f6c51b44fac3a508d712c25393%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636998498148426272sdata=hwa50qaC%2FS3Ma1o%2Bwy20l99PJ3mInnB%2FJqcX192PWvY%3Dreserved=0
>  <
>

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}

2019-07-29 Thread Greve, Douglas N.,Ph.D. 
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. 
> mailto:dgr...@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/MultipleComparisonsV6.0Perm
>> 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 >> > 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  
 

 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 
 https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Cb7ea74f6c51b44fac3a508d712c25393%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636998498148426272sdata=hwa50qaC%2FS3Ma1o%2Bwy20l99PJ3mInnB%2FJqcX192PWvY%3Dreserved=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
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu 
>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=02%7C01%7Cmark.wagshul%40einstein.yu.edu%7Ca32b0472033a420f1ea508d71397c21a%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636999414844382483sdata=kgZ%2Fj6%2BWbJxmAXz4mpdm6Z%2FZ2UHnnDSEswsPkGTFaVI%3Dreserved=0
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>

Re: [Freesurfer] Running FSL randomise on FS cortical thickness data {Disarmed}

2019-07-28 Thread Mark Wagshul 
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. 
mailto:dgr...@mgh.harvard.edu>> wrote:

FreeSurfer has its own permutation software
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
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 mailto:a...@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

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data

2019-07-28 Thread Greve, Douglas N.,Ph.D. 
FreeSurfer has its own permutation software
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
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 mailto:a...@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

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data

2019-07-27 Thread Mark Wagshul 
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 mailto:a...@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

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data

2019-07-27 Thread Antonin Skoch 
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___
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Freesurfer@nmr.mgh.harvard.edu
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