dcm_qa is a simple DICOM to NIfTI validator script and dataset. The DICOM format is the popular standard for medical images, but it is very complicated, so most scientific tools only support the simpler NIfTI format. Therefore, scientists rely on accurate conversion of DICOM images to NIfTI. The provided DICOM dataset includes images that exhibit various features such as variation in TotalReadoutTime, Slice Orientation and Transfer Syntax that might disrupt conversion (specific features are described in the text files). The current code validates dcm2niix, but could be easily adapted for other tools.
This validator script converts DICOM images in the "In" folders and saves the results in the "Out" folder. It then reports any differences between the "Out" folder and the "Ref" folder of reference files. It will report ANY differences between these files. This allows the script to check both NIfTI and BIDS format files. Note that just because there is a difference does not mean a conversion is incorrect. For example, the BIDS file contains the version of dcm2niix used for conversion, and one expects this to change with new versions. What this script does is report ALL changes, and the user can determine if they reflect regressions. For example, here is an example of a report where a different compiler (GCC vs CLANG) was used to generate dcm2niix:
--- /Users/rorden/dcm_qa/Out/sag_int_36sl_21.json 2017-06-21 12:36:48.000000000 -0400
+++ /Users/rorden/dcm_qa/Ref/sag_int_36sl_21.json 2017-06-21 09:11:20.000000000 -0400
@@ -26,5 +26,5 @@
"TrueEchoSpacing": 0.000559996,
"PhaseEncodingDirection": "i-",
"ConversionSoftware": "dcm2niix",
- "ConversionSoftwareVersion": "v1.0.20170621 GCC6.1.0"
+ "ConversionSoftwareVersion": "v1.0.20170621 Clang7.3.0"
}
This software and images are open source and were acquired by Chris Rorden. The the code is covered by the 2-clause BSD license and released in June 2017.
21-June-2017
- Initial public release
Assuming that the executable dcm2niix is in your path, you should be able to simply run the script batch.sh from the terminal.
If you have problems you can edit the first few lines of the batch.sh script so that basedir reports the explicit location of the dcm_qa folder (by default this is assumed to be the folder containing the script) on your computer and exenam reports the explicit location of dcm2niix (by default it is assumed to be in your path). Also, make sure the script is executable (chmod +x batch.sh). Then run the script.
This software reports when there are any changes in behavior of the software. However, some of these changes might be improvements. For example, software which supports future BIDS tags will report differences relative to the prior solutions reported in dcm_qa. Once the solutions have been verified as correct, one needs to update both dcm_qa and the software that invokes dcm_qa. For example, with dcm2niix we can update it to use the latest version of dcm_qa with this script:
cd dcm2niix
git submodule update --remote
git commit -am 'Update dcm_qa submodule.'
git push