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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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
> > >
> > 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> > https://secure-web.cisco.com/15gUXrKs3F3ttjgkvvhX-UHqb1JKlF-b2rzTvXEfrPDsA5o... >
>
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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: 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1B3HZiPg85_7DwP5_NbXcrOQ9op070zJAgcKpLacMVcU5sZ-fwsgoNDPZZn9lnbSHc1Wxg9a_dORpJaLEFbvSrw-GaOo1Lk1Ptm4pc2xDNyNbVYfx5lKRb5KCdFklcI5jPmLZUBSyJCbHtt-FSKpn29oPkhJsn5EzY20T7-HWHZ9qSl2-UnRer2NiKmsVschPm8MBZI5NAShpZQviGXqpVFV7o8oVO3EfCWTb8pSwntDuAMAcOXzUhVDaHEfd0hLN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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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:
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
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