Freesurfer tools have been adapted to work with species other than humans (e.g., dogs http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052140) but you cannot simply run the Freesurfer pipeline (recon-all). There are various sources of information that you can find using google to get you started (e.g., http://brainmeister.blogspot.fr/2010/06/freesurfer-on-macaque.html; https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData). Inside these you will see that the answer to your 2nd question is that you don’t reslice your data to 1mm but only change the information in the header to trick Freesurfer into thinking your data is 1mm. I’m not sure of the answer for question 3 but it would depend on the format your atlas is already in and how you wanted to use it.

On 15 Feb 2017, at 09:51, Arsene Ella <arsene.ella@inra.fr> wrote:

Hi everyone,

I am a newbie in freesurfer. I went a little bit throughout the tutorials and few questions arose:

1) Is freesurfer was only built to process data acquired on primates (especially humans)?
In other words, is freesurfer unable to process data from other animal models (rat, mouse, sheep....)?

2) Is a spatial resolution of 1mm iso voxel size a prerequisite for using freesurfer?
If my data have a better spatial resolution (0.5 mm iso voxel size for example), do they necessarily have to be transformed to a resolution of 1mm iso voxel prior to be used in freesurfer?

3) If I want to use my own atlas in freesurfer, in which form (label, annotation, format ...) should it be? And in which directory do I have to put it?

I would really appreciate any help.

Thanks.

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