Re: [Freesurfer] Myelinated cortical thickness ratio map

2018-11-07 Thread Greve, Douglas N.,Ph.D. 
You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search 
through the mail archives for how to use it

On 10/23/2018 06:34 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi Matt,
>
> Many thanks for your prompt reply, you are right.
>
> Any tips on how I could do that?
>
> Should I regress out cortical thickness from my myelin maps at the 
> individual level, save the individual output myelin maps and run 
> analyses on the latter? If yes how?
>
> That’s really important to me otherwise a reviewer could claim the 
> myelin differences we detect might be supported by cortical thickness 
> variations and not myelin…
>
> Thank you and best,
>
> Damien
>
>
>
>> Glasser, Matthew 
>> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Glasser%2C+Matthew%22>Mon,
>>  
>> 22 Oct 2018 12:57:43 -0700 
>> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20181022>
>>
>> Regression would be better than division.
>> Matt.
>>
>> From:
>> > <http://nmr.mgh.harvard.edu/><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>>   on behalf of Damien MARIE http://damien.ma/>...@unige.ch 
>> <http://unige.ch/><mailto:damien.ma...@unige.ch>>
>> Reply-To: Freesurfer support list
>> > <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Date: Monday, October 22, 2018 at 8:54 AM
>> To: "freesurfer@nmr.mgh.harvard.edu 
>> <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>"
>>  
>> > <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [Freesurfer] Myelinated cortical thickness ratio map
>>
>>
>>  External Email - Use Caution
>>
>> Dear experts,
>>
>> I am working with R1 maps that I project on the surface. The goal is to look 
>> at
>> intra-cortical myelin.
>>
>> I detect interesting effects between two groups. Now I would like to compute
>> myelinated cortical thickness ratio maps, in order to control for the effect 
>> of
>> cortical thickness variations occurring with gyrification.
>>
>> Here is a paper where they describe a way to compute those myelinated 
>> cortical
>> thickness ratio map with MIPAV and the MPI-CBS toolbox :
>> https://www.ncbi.nlm.nih.gov/pubmed/29321232
>> «  The proportional thickness of the myelinated part of the cortex in 
>> relation
>> to its overall thickness (myelinated cortical thickness) was computed with a
>> fuzzy classification technique combining information about radial and
>> tangential fibers.  «
>>
>> 1- Is it possible to do the same in FreeSurfer?
>>
>> 2- What about dividing my individual myelin maps by the individual cortical
>> thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do
>> the job in the volume but I don’t know how I could do that in FreeSurfer.
>>
>> Any comments / other suggestions are welcome.
>>
>> Thank you and best,
>>
>> Damien
>>
>
>
>
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Re: [Freesurfer] Myelinated cortical thickness ratio map

2018-10-23 Thread Damien MARIE 
External Email - Use Caution

Hi Matt,

Many thanks for your prompt reply, you are right.

Any tips on how I could do that?

Should I regress out cortical thickness from my myelin maps at the individual 
level, save the individual output myelin maps and run analyses on the latter? 
If yes how?

That’s really important to me otherwise a reviewer could claim the myelin 
differences we detect might be supported by cortical thickness variations and 
not myelin…

Thank you and best,

Damien



> Glasser, Matthew 
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Glasser%2C+Matthew%22>
>  Mon, 22 Oct 2018 12:57:43 -0700 
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20181022>
> 
> Regression would be better than division.
> Matt.
> 
> From: 
>  <http://nmr.mgh.harvard.edu/><mailto:freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>>
>  on behalf of Damien MARIE http://damien.ma/>...@unige.ch 
> <http://unige.ch/><mailto:damien.ma...@unige.ch 
> <mailto:damien.ma...@unige.ch>>>
> Reply-To: Freesurfer support list 
>  <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> Date: Monday, October 22, 2018 at 8:54 AM
> To: "freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>" 
>  <mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> Subject: [Freesurfer] Myelinated cortical thickness ratio map
> 
> 
> External Email - Use Caution
> 
> Dear experts,
> 
> I am working with R1 maps that I project on the surface. The goal is to look 
> at 
> intra-cortical myelin.
> 
> I detect interesting effects between two groups. Now I would like to compute 
> myelinated cortical thickness ratio maps, in order to control for the effect 
> of 
> cortical thickness variations occurring with gyrification.
> 
> Here is a paper where they describe a way to compute those myelinated 
> cortical 
> thickness ratio map with MIPAV and the MPI-CBS toolbox : 
> https://www.ncbi.nlm.nih.gov/pubmed/29321232 
> <https://www.ncbi.nlm.nih.gov/pubmed/29321232>
> «  The proportional thickness of the myelinated part of the cortex in 
> relation 
> to its overall thickness (myelinated cortical thickness) was computed with a 
> fuzzy classification technique combining information about radial and 
> tangential fibers.  «
> 
> 1- Is it possible to do the same in FreeSurfer?
> 
> 2- What about dividing my individual myelin maps by the individual cortical 
> thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
> the job in the volume but I don’t know how I could do that in FreeSurfer.
> 
> Any comments / other suggestions are welcome.
> 
> Thank you and best,
> 
> Damien
> 

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Re: [Freesurfer] Myelinated cortical thickness ratio map

2018-10-22 Thread Glasser, Matthew 
External Email - Use Caution

Regression would be better than division.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Damien MARIE mailto:damien.ma...@unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, October 22, 2018 at 8:54 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Myelinated cortical thickness ratio map


External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232
«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  «

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien




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[Freesurfer] Myelinated cortical thickness ratio map

2018-10-22 Thread Damien MARIE 
External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.  

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232 

«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  « 

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien
 
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