Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Douglas Greve]

I'm not sure what this is referring to, but you should be very careful 
flipping images. If you want to compare left and right, then use the 
xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi


On 9/4/18 10:41 AM, Martin Reuter wrote:

Hi Xiaoyu,

please keep the previous conversation as inline citation below so I 
know what we discussed before.


What I mean is to process every subject only once and not twice (with 
flipped images, if that is what you did?).


Then run xhemi analysis on the subject-level. Invert the sign of the 
left-right difference depending on which is the diseased hemi. Then do 
a regular analysis on that. Nothing paired.


Best, Martin



On 30. Aug 2018, at 18:29, Wang, Xiaoyu 
> wrote:




Thanks Martin,
Yes, I did mean to have the right hemisphere added to the left 
hemisphere as a new time point.

Can you explain on what you mean by run every subject only once?
Do you mean to run xhemi for all of the subjects and then run a 
paired analysis?

Xiaoyu
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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Martin Reuter]

Hi Xiaoyu, 

please keep the previous conversation as inline citation below so I know what 
we discussed before. 

What I mean is to process every subject only once and not twice (with flipped 
images, if that is what you did?). 

Then run xhemi analysis on the subject-level. Invert the sign of the left-right 
difference depending on which is the diseased hemi. Then do a regular analysis 
on that. Nothing paired. 

Best, Martin



> On 30. Aug 2018, at 18:29, Wang, Xiaoyu  
> wrote:
> 
> 
> 
> 
> Thanks Martin,
>  
> Yes, I did mean to have the right hemisphere added to the left hemisphere as 
> a new time point.
>  
> Can you explain on what you mean by run every subject only once?
> Do you mean to run xhemi for all of the subjects and then run a paired 
> analysis?
>  
> Xiaoyu
>  
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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Wang, Xiaoyu]

External Email - Use Caution

Thanks Martin,

Yes, I did mean to have the right hemisphere added to the left hemisphere as a 
new time point.

Can you explain on what you mean by run every subject only once?
Do you mean to run xhemi for all of the subjects and then run a paired analysis?

Xiaoyu

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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

[Martin Reuter]

Hi Xiaoyu, 

I don't think it makes sense to model the hemisphere each as a
different group. Do you mean different time point?

The problem is that left hemispheres are probably anatomically slightly
different than right hemispheres (on average in healthy people). 

I would run every subject only once, then do a x-hemi analysis (I think
there are tools for that, which try to keep stuff unbiased with respect
to the hemi) and then perform your statistic on that.

Since not all diseased hemispheres are on one side, it makes sense to
attach a sign to the x-hemi difference so that you always have, e.g.
healthy-diseased. Then simply do a GLM on that. 

Best, Martin


On Tue, 2018-08-28 at 22:18 +, Wang, Xiaoyu wrote:
>   
> Hello Freesurfer Experts,
>  
> I am trying to compare the left and right hemisphere of a group of PD
> patients with Mass-Univarate LME.
>  
> From what I can see in the wiki tutorial, the mris_preproc only
> assembles data from one hemisphere at a time, which is not very
> usefull if I am doing a hemisphere comparison where each hemisphere
> is a different group.
>  
> I am thinking of getting around this issue by flipping each subject
> time point so that the right hemisphere is on the left and adding it
> as a new timepoint.
> For example:
> S01_1    s01_base
> S01_1f  s01_base
> S01_2    s01_base
> S01_2f  s01_base
>  
> However, Can I still create the base file the same way using this?
>   recon-all -base  -tp  -tp  ... -all
>  
> also for the fsaverage, would make_average_subject still work?
>  
> Xiaoyu
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[Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal Comparison

[Wang, Xiaoyu]

External Email - Use Caution

Hello Freesurfer Experts,

I am trying to compare the left and right hemisphere of a group of PD patients 
with Mass-Univarate LME.

>From what I can see in the wiki tutorial, the mris_preproc only assembles data 
>from one hemisphere at a time, which is not very usefull if I am doing a 
>hemisphere comparison where each hemisphere is a different group.

I am thinking of getting around this issue by flipping each subject time point 
so that the right hemisphere is on the left and adding it as a new timepoint.
For example:
S01_1s01_base
S01_1f  s01_base
S01_2s01_base
S01_2f  s01_base

However, Can I still create the base file the same way using this?
  recon-all -base  -tp  -tp  ... -all

also for the fsaverage, would make_average_subject still work?

Xiaoyu
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