[Freesurfer] Running recon-all on dicom/IMA files within the same study

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Hi FreeSurfer devs,

Thanks for the program! I am assisting in a study comparing structural neuroimaging data between groups. Some of the MRI files exist as .dcm, while others exist as .IMA. Given the variability in FreeSurfer outputs noted here: https://secure-web.cisco.com/1_vxoF_SONV8dZuTkJbocobHWUZzyYP1cLrpyTK0qXC1WT_..., is it a sound practice for me to run recon-all on both dicom and IMA files within the same study? Or should I convert all files to NIFTI, and run analyses on those files (to eliminate the potential influence of filetype on output)?

I only ask because I've already run recon-all on quite a few IMA files, and would have to re-do these scripts if it's better for me to convert to nifti first.

I look forward to your response, and thanks again for all the work that you lot do! Nate