External Email - Use Caution
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.
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:
External Email - Use Caution
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use Caution
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vXczG4CAmxjEcjCX1H0-KH3Kyl1RHOfECCW2w4kaAj_7O3...https://secure-web.cisco.com/1TXB_MEwP1Lg8puaOTLUdXwIfxZTMOx3QXs-37cirZaSKZslBLbdzqGiwhoLINAPeM3fxi3XIhaG2AYF0PIWkUD4kF2sNufWzNGmjOePp8MldQIvV2-giNpsPC8GOg2tMH7gA92Zr5TUsN9wDyCsdKum-Uphm3B4iE59EjOfNzRW8s6GWY7tSs42ZrdnjvpMRwxYGR8rX9DhHjcB6HirtLMbuTMzcb9-V4X5-5Ck9kbNUA0MOrqCwYNTnrgee7SJn/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMDaQ%26c%3DZQs-KZ8oxEw0p81sqgiaRA%26r%3Do8G9kgCzcd-6BbsbeKDQ9Q%26m%3DjqOvJoFRgzf_OWb_CDzsCOznIStVB4HefoDGSO0slaU%26s%3DvIXQVKe3iEZbfQR37nGbv4hDNRW1x3fS3XMJ82f-T_E%26e%3D
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Rizzo, Nolan W