It might be that the format is too new for our code. Have you tried dcm2niix? We are currently incorporating dcm2niix backend into mri_convert, but we're not there yet.

On 10/6/2021 2:36 PM, Rizzo, Nolan W wrote:

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Hello FreeSurfer developers,

I am attempting to use mri_convert to convert DICOM files to a NIfTI file. The DICOM images were obtained from a Siemens 3T Prisma scanner with VE11C software version. When mri_convert is run to convert the .dcm files to .nii , an error occurs that displays "bad fd number". I believe the problem occurs when mri_convert is trying to decompress the new JPEG format of the DICOM files. I have listed the FreeSurfer version and OS that I used below.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

Platform: Ubuntu 16.04

This error did not occur when running mri_convert on the Mac version of FreeSurfer using OS Mojave. The same DICOM files (as above) were used. mri_convert ran without error and produced the .nii file.

Thank you.
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