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