In general, FreeSurfer does not care what orientation your images are in as long as the geometry in the header file is correct. If you re-oriented them for SPM and you are confident that the geometry info is still correct (eg, no left-right flips) and you did not change the scale of the images (ie, no stretching or compression to get into talairach space), then you should be able to run FS on them without problem. For FSFAST, there is no need to reorient.

On 04/12/2016 10:59 AM, Julio Alberto González Torre wrote:

Hi Freesurfer users.

I performed the recomended reconstruction of 82 subjects with Freesurfer.

The images used for this reconstruction were previously reoriented to AC-PC position, because they were previously used for SPM purposes.

Now I'm trying to perform the FSFAST workflow, and I had to unpack the original functional DICOMs for each subject. Those images are not reoriented because they were not used until now.

The question is: The functional images should be previously reoriented to the same position as the anatomical used in Freesurfer?

Should I perform the recomended reconstruction again with the original DICOMS?

Or it doesn't matter the reorientation of the functional/anatomical images and Freesurfer would perform correctly the FSFAST? (I hope so, so I could skip the reconstruction, which involves many hours of processing)

Thanks.

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