[Neuroimaging] Integrating Freesurfer with Python

Yaroslav Halchenko lists at onerussian.com
Mon Sep 4 10:24:56 EDT 2017


On Mon, 04 Sep 2017, Maksimovskiy, Arkadiy wrote:

>    Hi Everyone,



>    My apologies for the basic question. I am a beginner at integrating
>    Freesurfer commands into python scripts, and was wondering if anyone has
>    suggestions on what would be the best way to do it. Specifically, for a
>    python program that uses Freesurfer commands, is it possible to source
>    Freesurfer within the python script and then use the commands? Or does
>    sourcing the environment need to happen prior to running such scripts?

have you looked into using nipype?
http://nipype.readthedocs.io/en/latest/
it provides interfaces for the majority of open source toolkits in
neuroimaging (freesurfer included) and a number of precrafted analysis
pipelines

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        


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