External Email - Use Caution Dear Freesurfer support team,
I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view. I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “. Any help is much appreciated Kind regards, Jeiran Jeiran Choupan, PhD, MSCS Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California 2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN [image001.png] [image002.png]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
