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I have not tried dcmi2niix yet. I will see if this works for the files.
Thank you. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, October 8, 2021 12:37 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error using mri_convert
***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe. ________________________________ 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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