subject:"Re\: \[Freesurfer\] GLM in groups with unequal size"

Re: [Freesurfer] GLM in groups with unequal size

2016-10-14 Thread Douglas Greve

It will not

On 10/13/16 10:34 AM, Eelco van Duinkerken wrote:
Ah sorry for the low level of info. I am aiming to do a simple group 
comparison, where I'm comparing thickness between controls and obese 
or T2DM patients, regressing out the effect of age, sex and, 
hypertension. So I created one thickness file with fwhm 10 containing 
all participants of the 3 groups.

The contrast file looks like this:

1 0 -1 0 0 0 for controls vs T2DM
1 -1 0 0 0 0 for controls vs obese
0 1 -1 0 0 0 for obese vs T2DM, although there I do not expect 
something to happen

And the GLM works fine (differences in the first and second contrast), 
but I was wondering whether the fact that the groups are unbalanced 
might influence the results in some way.

Thanks,

Eelco

2016-10-13 11:17 GMT-03:00 Bruce Fischl >:

Hi Eelco

it depends on how you setup your GLM. Are you trying to regress
out the effects of obesity in some way? If you give us more
details I expect someone else can answer your question (Doug!)

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

Thanks for the quick reply!
So if I understand correctly, the power of say the controls
vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by
the sample size
of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>:
  Hi Eelco

  it isn't really a question of whether our implementation is
  senstitive to
  this. It's that in general your power will be
constrained by the
  size of
  the smaller group (I assume this is Type 2 diabetes by
the way).

  cheers
  Bruce

  On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

  > Hi all,
  > I am using FS with data from 2 different studies that were
  acquired on the
  > same MRI-machine with the same T1 and FLAIR sequences.
  Unfortunately, the
  > group sizes are not very balanced, with 31 controls,
16 obese
  and 32
  > diabetes patients.
  >
  > Is the GLM for thickness used in FS very sensitive to this
  unequal group
  > size?
  >
  >
  > Thanks for the help,
  >
  > Eelco
  >
  >
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--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ |
CEP 22451-900 |
Brasil |
E-mail: e.vanduinker...@vumc.nl
 | Phone: +55-21-35271855
 |
http://lattes.cnpq.br/7180895567820901

&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gáv

Re: [Freesurfer] GLM in groups with unequal size

2016-10-14 Thread Douglas Greve

It will be constrained by the group with the smaller number of subjects. 
There is not anything wrong with unequal group sizes, but it is less 
efficient than if you had split your acquisitions evenly.

On 10/13/16 10:17 AM, Bruce Fischl wrote:

Hi Eelco

it depends on how you setup your GLM. Are you trying to regress out 
the effects of obesity in some way? If you give us more details I 
expect someone else can answer your question (Doug!)

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

Thanks for the quick reply!
So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the 
sample size

of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl :
  Hi Eelco

  it isn't really a question of whether our implementation is
  senstitive to
  this. It's that in general your power will be constrained by the
  size of
  the smaller group (I assume this is Type 2 diabetes by the way).

  cheers
  Bruce

  On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

  > Hi all,
  > I am using FS with data from 2 different studies that were
  acquired on the
  > same MRI-machine with the same T1 and FLAIR sequences.
  Unfortunately, the
  > group sizes are not very balanced, with 31 controls, 16 obese
  and 32
  > diabetes patients.
  >
  > Is the GLM for thickness used in FS very sensitive to this
  unequal group
  > size?
  >
  >
  > Thanks for the help,
  >
  > Eelco
  >
  >
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--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 
22451-900 |

Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Eelco van Duinkerken

Thank you Jurgen!
That helps a lot. Good to know that the results are not driven by any
difference in varience.

Thanks all,

Eelco

2016-10-13 12:00 GMT-03:00 Juergen Haenggi :

> Dear Eelco
>
> years ago i posed a similar question on the FS email list
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
> 2011-November/021386.html
>
> a part of the response is below
>
> >>>* The other question is how mri_glmfit estimates the variance. Because I 
> >>>have
> *>>>* only one subject in the patient group, there is not variance in that 
> group
> *>>>* and therefore I guess mri_glmfit used pooled (across both groups) 
> estimates
> *>>>* of variance, isn't it?
> *>>>   >>>   >>* Yes, it uses pooled estimates.
> ** doug*
>
> if you are concerned with respect to the variance estimates, it does not
> matter because variance is estimated pooledly, i.e. across both groups.
> hope this helps
>
> Cheers
> Jürgen
>
> 
> -
> University of Zurich
> Dr. Jürgen Hänggi, Ph.D.
> Department of Psychology
> Division Neuropsychology
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
>
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
>
> j.haen...@psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
> 
> -
>
>
>
>
> Am 13.10.2016 um 15:56 schrieb Eelco van Duinkerken:
>
> Hi all,
>
> I am using FS with data from 2 different studies that were acquired on the
> same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the
> group sizes are not very balanced, with 31 controls, 16 obese and 32
> diabetes patients.
>
> Is the GLM for thickness used in FS very sensitive to this unequal group
> size?
>
>
> Thanks for the help,
>
> Eelco
> ___
> Freesurfer mailing list
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>
>
> 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
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> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
> ___
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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> properly
> dispose of the e-mail.
>
>


-- 
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900
| Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands
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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Juergen Haenggi

Dear Eelco

years ago i posed a similar question on the FS email list

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021386.html

a part of the response is below

>>> The other question is how mri_glmfit estimates the variance. Because I have
>>> only one subject in the patient group, there is not variance in that group
>>> and therefore I guess mri_glmfit used pooled (across both groups) estimates
>>> of variance, isn't it?
>>>   
>>>   
>> Yes, it uses pooled estimates.
>>
>> doug
if you are concerned with respect to the variance estimates, it does not matter 
because variance is estimated pooledly, i.e. across both groups.
hope this helps

Cheers
Jürgen

-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)   
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number) 

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
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material in this e-mail is strictly forbidden.
-




Am 13.10.2016 um 15:56 schrieb Eelco van Duinkerken:

> Hi all,
> 
> I am using FS with data from 2 different studies that were acquired on the 
> same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the 
> group sizes are not very balanced, with 31 controls, 16 obese and 32 diabetes 
> patients.
> 
> Is the GLM for thickness used in FS very sensitive to this unequal group size?
> 
> 
> Thanks for the help,
> 
> Eelco
> ___
> 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.

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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Eelco van Duinkerken

Ah sorry for the low level of info. I am aiming to do a simple group
comparison, where I'm comparing thickness between controls and obese or
T2DM patients, regressing out the effect of age, sex and, hypertension. So
I created one thickness file with fwhm 10 containing all participants of
the 3 groups.
The contrast file looks like this:

1 0 -1 0 0 0 for controls vs T2DM
1 -1 0 0 0 0 for controls vs obese
0 1 -1 0 0 0 for obese vs T2DM, although there I do not expect something to
happen

And the GLM works fine (differences in the first and second contrast), but
I was wondering whether the fact that the groups are unbalanced might
influence the results in some way.

Thanks,

Eelco




2016-10-13 11:17 GMT-03:00 Bruce Fischl :

> Hi Eelco
>
> it depends on how you setup your GLM. Are you trying to regress out the
> effects of obesity in some way? If you give us more details I expect
> someone else can answer your question (Doug!)
>
>
> cheers
> Bruce
>
>
> On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:
>
> Thanks for the quick reply!
>> So if I understand correctly, the power of say the controls vs. diabetes
>> (indeed it is type 2 diabetes) comparison is constrained by the sample
>> size
>> of the obese group?
>>
>> 2016-10-13 11:02 GMT-03:00 Bruce Fischl :
>>   Hi Eelco
>>
>>   it isn't really a question of whether our implementation is
>>   senstitive to
>>   this. It's that in general your power will be constrained by the
>>   size of
>>   the smaller group (I assume this is Type 2 diabetes by the way).
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:
>>
>>   > Hi all,
>>   > I am using FS with data from 2 different studies that were
>>   acquired on the
>>   > same MRI-machine with the same T1 and FLAIR sequences.
>>   Unfortunately, the
>>   > group sizes are not very balanced, with 31 controls, 16 obese
>>   and 32
>>   > diabetes patients.
>>   >
>>   > Is the GLM for thickness used in FS very sensitive to this
>>   unequal group
>>   > size?
>>   >
>>   >
>>   > Thanks for the help,
>>   >
>>   > Eelco
>>   >
>>   >
>> ___
>> 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.
>>
>>
>>
>>
>> --
>> Eelco van Duinkerken, PhD
>> Pontifícia Universidade Católica | Department of Psychology |
>> R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP
>> 22451-900 |
>> Brasil |
>> E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
>> http://lattes.cnpq.br/7180895567820901
>> &
>> VU University Medical Center | Department of Medical Psychology |
>> De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands
>>
>>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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>


-- 
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900
| Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands
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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Eelco van Duinkerken

Thanks for the quick reply!

So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the sample size
of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl :

> Hi Eelco
>
> it isn't really a question of whether our implementation is senstitive to
> this. It's that in general your power will be constrained by the size of
> the smaller group (I assume this is Type 2 diabetes by the way).
>
> cheers
> Bruce
>
>
> On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:
>
> > Hi all,
> > I am using FS with data from 2 different studies that were acquired on
> the
> > same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the
> > group sizes are not very balanced, with 31 controls, 16 obese and 32
> > diabetes patients.
> >
> > Is the GLM for thickness used in FS very sensitive to this unequal group
> > size?
> >
> >
> > Thanks for the help,
> >
> > Eelco
> >
> >
> ___
> 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.
>
>


-- 
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900
| Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands
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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Bruce Fischl

Hi Eelco

it depends on how you setup your GLM. Are you trying to regress out the 
effects of obesity in some way? If you give us more details I expect 
someone else can answer your question (Doug!)

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken 
wrote:

Thanks for the quick reply!
So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the sample size
of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl :
  Hi Eelco

  it isn't really a question of whether our implementation is
  senstitive to
  this. It's that in general your power will be constrained by the
  size of
  the smaller group (I assume this is Type 2 diabetes by the way).

  cheers
  Bruce

  On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

  > Hi all,
  > I am using FS with data from 2 different studies that were
  acquired on the
  > same MRI-machine with the same T1 and FLAIR sequences.
  Unfortunately, the
  > group sizes are not very balanced, with 31 controls, 16 obese
  and 32
  > diabetes patients.
  >
  > Is the GLM for thickness used in FS very sensitive to this
  unequal group
  > size?
  >
  >
  > Thanks for the help,
  >
  > Eelco
  >
  >
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contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.

--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology | 
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900 |
Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology | 
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Re: [Freesurfer] GLM in groups with unequal size

2016-10-13 Thread Bruce Fischl

Hi Eelco

it isn't really a question of whether our implementation is senstitive to 
this. It's that in general your power will be constrained by the size of 
the smaller group (I assume this is Type 2 diabetes by the way).

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

> Hi all,
> I am using FS with data from 2 different studies that were acquired on the
> same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the
> group sizes are not very balanced, with 31 controls, 16 obese and 32
> diabetes patients.
> 
> Is the GLM for thickness used in FS very sensitive to this unequal group
> size?
> 
> 
> Thanks for the help,
> 
> Eelco
> 
>
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Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

Re: [Freesurfer] GLM in groups with unequal size

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