Re: [Freesurfer] Cortical thickness average

[Douglas N Greve]

mri_concat subject1/lh.thickness.fsaverage.mgh subect2/lh ... --mean --o 
lh.thickness.fsaverage.mean.mgh


On 03/24/2016 07:24 PM, Sahil Bajaj wrote:
> Hello FreeSurfer community,
>
> I calculated cortical thickness for 100 controls following the 
> instructions described here: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
> So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was 
> wondering if there is any way to average the thickness over these 100 
> lh.thickness.fsaverage.mgh files to get one final 
> lh.thickness.fsaverage.mgh
>
> I am interested in calculating cortical thickness for 15 previously 
> defined ROIs, but I do not want to calculate 15x100 text files using 
> mri_segstats i.e. 15 text files for each subject and then average over 
> those but I would rather prefer to average over 100 
> lh.thickness.fsaverage.mgh files first and then calculate thickness 
> for each ROI to get 11 text files.
>
> Any help would be really appreciated.
>
> Thanks,
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.br...@gmail.com 
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Cortical thickness average

[Sahil Bajaj]

Thanks a lot Elijah, I will give a try to this and will surely get back to
you if I had any issue.

Thanks again for the help.

Regards,
Sahil

On Thu, Mar 24, 2016 at 6:39 PM, Elijah Mak  wrote:

> Hi Sahil,
>
> I did something similar recently. I believe you can use mri_concat with
> the -mean option to create an average map of the group.
>
> Another option might be make_average_subject?
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject
>
> Best Wishes,
> Elijah
>
>
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> is
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> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> dispose of the e-mail.
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>


-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Cortical thickness average

[Elijah Mak]

Hi Sahil,

I did something similar recently. I believe you can use mri_concat with the
-mean option to create an average map of the group.

Another option might be make_average_subject?

https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject

Best Wishes,
Elijah
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