Hi,
Yes, fsl_anat uses run_first_all, so it doesn't matter if you run this yourself outside of fsl_anat (using the bias-corrected image from fsl_anat).
All the best,
Mark
On 19 Jul 2013, at 17:56, Nate MW <[log in to unmask]> wrote:
> Just to follow up on this intermittent bug, I have also ran into it and will follow Mark's suggestion to use run_first_all for two of my subjects for whom fsl_anat did not work. Is it common to have a mix of first_seg files in which some came from run_first_all and others came from fsl_anat? I think I've read in the forum that fsl_anat is using run_first_all, but I wasn't sure if anyone has done direct comparisons on the results for the same subjects using both fsl_anat and run_first_all.
>
> Thanks,
> Nate
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