Hi Nate

I guess it depends on how they were created. If it the ima/dicom creation doesn't change either the direction cosines or the image data I don't think it should be a problem.

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Nathan Hostetler Sent: Wednesday, May 26, 2021 9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Running recon-all on dicom/IMA files within the same study

External Email - Use Caution

External Email - Use Caution 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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234https://secure-web.cisco.com/1_vxoF_SONV8dZuTkJbocobHWUZzyYP1cLrpyTK0qXC1WT__JHZ-EmKWVOouDaQIxdX9rKjG03L7V_q9yXLSx5jAArzFsODFNTP2fNYVKl8Sy6qSPQAlTTliYz3WDJmXtxBi8dDhAcKNZNtR6w97c2QCx6hnFV1fHmxkwetSdRL1bqSDLaBlErmZvkxbCbyTwETzd-gtIowaGpLqGKioDdc7P1093WISpeOTCRbIwdMLLAZ4kWpAqbmX23NchHsY6gsJEbSBlAytTpuR5DHP9Qw/https%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%2Fjournal.pone.0038234, 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