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Feb 6, 2019 02:02 PM | Tom Bresser
dcm2niix error when converting a Phillips DTI .PAR
Hi all,
Our lab uses dcm2niix to convert the PAR/REC files into nifti.
In our new study we have an updated DTI sequence that has thee b-value within the same file (b0 images, b1000 and b2000).
When I run dcm2niix (with the -z y and -s y) on the PAR file, I receive the following error
Using dcm2nii or the DICOM file from the scan produces no error and creates a .nii.gz file.
Do you know what is causing this error and why it is not present when using the DICOM files?
Kind regards,
Tom
Our lab uses dcm2niix to convert the PAR/REC files into nifti.
In our new study we have an updated DTI sequence that has thee b-value within the same file (b0 images, b1000 and b2000).
When I run dcm2niix (with the -z y and -s y) on the PAR file, I receive the following error
Compression will be faster with 'pigz' installed
http://macappstore.org/pigz/
Chris Rorden's dcm2niiX version v1.0.20181125 Clang10.0.0 (64-bit MacOS)
Warning: dcm2niix PAR is not actively supported (hint: use dicm2nii)
Error: Use dicm2nii or increase kMaxDTI4D to be more than 65340
slices*grad*bval*cardiac*echo*dynamic*mix*label = 66*90*11*1*1*1*1*1
Chris Rorden's dcm2niiX version v1.0.20181125 Clang10.0.0 (64-bit MacOS)
Warning: dcm2niix PAR is not actively supported (hint: use dicm2nii)
Error: Use dicm2nii or increase kMaxDTI4D to be more than 65340
slices*grad*bval*cardiac*echo*dynamic*mix*label = 66*90*11*1*1*1*1*1
Using dcm2nii or the DICOM file from the scan produces no error and creates a .nii.gz file.
Do you know what is causing this error and why it is not present when using the DICOM files?
Kind regards,
Tom
Feb 6, 2019 03:02 PM | Chris Rorden
RE: dcm2niix error when converting a Phillips DTI .PAR
Hard to say without seeing your data.
I would suggest try one of these options
1. Export data as DICOM. Since Philips has deprecated PAR/REC this seems wise, and would provide archival quality datasets.
2. You are using the latest stable dcm2niix release. However, there are a few minor changes to the PAR/REC conversion are in the development branch. I would compile the latest development commit. If you use Windows, go to the dcm2niix github page, select the "Development" branch, click the green AppVeyor button and click artifacts to get a compiled version. If you use Linux/MacOS:
$ git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
$ cd dcm2niix/console
$ make
$ ./dcm2niix
3. Follow the advice provided and try the outstanding dicm2nii
https://github.com/xiangruili/dicm2nii
I would suggest try one of these options
1. Export data as DICOM. Since Philips has deprecated PAR/REC this seems wise, and would provide archival quality datasets.
2. You are using the latest stable dcm2niix release. However, there are a few minor changes to the PAR/REC conversion are in the development branch. I would compile the latest development commit. If you use Windows, go to the dcm2niix github page, select the "Development" branch, click the green AppVeyor button and click artifacts to get a compiled version. If you use Linux/MacOS:
$ git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
$ cd dcm2niix/console
$ make
$ ./dcm2niix
3. Follow the advice provided and try the outstanding dicm2nii
https://github.com/xiangruili/dicm2nii
Feb 20, 2019 12:02 PM | Tom Bresser
RE: dcm2niix error when converting a Phillips DTI .PAR
Hi Chris,
Thanks for the reply. We will try out the options. The deprecation of PAR/REC by Philips forms a concern, because so far we archive data as PAR/REC. Fortunatly most of the data is still available in DICOM.
Kind regards,
Tom
Thanks for the reply. We will try out the options. The deprecation of PAR/REC by Philips forms a concern, because so far we archive data as PAR/REC. Fortunatly most of the data is still available in DICOM.
Kind regards,
Tom