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Yes, it runs to completion with --no-dwi. And for now, we don't need the bvals and bvects. 

Thanks a lot for your help!

On 26.01.2021 16:16, Douglas N. Greve wrote:

It throws an error when trying to extract the bvals or bvects. Can you try it with --no-dwi and see if it runs to completion? If it does, do you have another way to get the bvals and bvects?

On 1/26/2021 3:33 AM, Hannah Eichhorn wrote:

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Thanks for your answer!

 

The full command line is:

 

mri_convert /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii

 

And the terminal output:

 

mri_convert /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031.nii 

reading from /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA...

INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom.

If this fails, run mri_convert with -it dicom

Getting Series No 

Scanning Directory 

INFO: Found 29 files in /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031

INFO: Scanning for Series Number 31

INFO: found 27 files in series

INFO: loading series header info.

ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7

DICOM File: /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA

break /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639

ERROR: reading /indirect/data1/hannah/Test/RESOLVE_3SCAN_TRACE_TRA_P2_160_ADC_0031/MR.MOCO_TRACOLINE_TEST.0031.0001.2021.01.13.12.54.51.790046.85818469.IMA 

INFO: sorting.

Segmentation fault (core dumped)

 

Best regards,

Hannah

 

 

Am 26.01.2021 04:23:58, schrieb Douglas N. Greve:

Can you send the full command line and terminal output?

On 1/22/2021 4:29 AM, Hannah Eichhorn wrote:

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Dear all,

 

I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty format, but I get the following error when I run the mri_convert Test.IMA Test.nii command:

 

ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7 

DICOM File: Test.IMA 

break /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639 

ERROR: reading Test.IMA 

INFO: sorting. 

Segmentation fault (core dumped)

I have searched the mail archive and didn't find similar errors. Does anyone have any thoughts on how to solve this error?

I am using FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

Thank you,

Hannah Eichhorn

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