External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PT1JeE9nKor9Jut5X5X8rp6U79iUv9Z8GXFTshKWYlGuDh... [1]
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PT1JeE9nKor9Jut5X5X8rp6U79iUv9Z8GXFTshKWYlGuDh... [1]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1PT1JeE9nKor9Jut5X5X8rp6U79iUv9Z8GXFTshKWYlGuDh...
Links: ------ [1] https://secure-web.cisco.com/1B3HZiPg85_7DwP5_NbXcrOQ9op070zJAgcKpLacMVcU5sZ...