dcm_qa_philips_asl is a simple DICOM to NIfTI validator script and dataset. This repository is similar to dcm_qa, but includes data from Philips MRI scanners. Specifically, this dataset uses Arterial Spin Labeling (ASL). For ASL data from a Siemens scanner see dcm_qa_asl.
The image in this repsoitory were exported as enhanced DICOMs, to see the same datastet saved in classic format see dcm_qa_philips_asl.
Data provided by Paul S. Morgan at the University of Nottigham. Data was saved as both classic (where each slice is a separate file) as well as enhanced DICOM (where an entire series of images is saved as a single file) format. Each ASL series is saved as both a volume that shows the average difference between the label and control images (e.g. series 201) and the raw data for that series (e.g. series 202).
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Common Parameters
- Manufacturer: Philips
- Model: Ingenia Elition X
- Implementation Version: Philips MR 57.0
- Software Versions: 5.7.1.2
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20x_pCASL- Technique: 2D Pseudo-Continuous Arterial Spin Labeling (pCASL)
- Volumes: 60 (30 repeats: half label, half control)
- Post Label Delay (ms): 1800
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30x_ASL_MultiPhase- Technique: STAR Pulsed Arterial Spin Labeling (PASL)
- Volumes: 480 (8 phases, 30 repeats: half label, half control)
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40x_3D_pCASL_6mm- Technique: 3D Pseudo-Continuous Arterial Spin Labeling (pCASL)
- Volumes: 16 (8 repeats: half label, half control)
- Post Label Delay (ms): 2000
The BIDS BEP005 provides recommended and required sequence parameters for analysis of Arterial Spin Labeling (ASL). The Philips DICOM headers do not provide many of these values. Therefore, one should carefully document sequence settings when setting up Philips ASL scans.
There are a number of quirks in the data. These features do not seem to fit a simple interpretation of the DICOM standard. Therefore, to allow automatic processing of these datasets, dcm2niix must make a few assumptions. This may make dcm2niix somewhat fragile for this modality.
The enhanced DICOMs list the difference images (series 201, 301, 401) as having a REAL Complex Image Component (0008,9208) but the classic scans do not.
Philips ASL scans seem to suggest a cardiac gated trigger. For example, consider the enhanced DICOM for series 301 and 302:
(0018,9037) CS [PROSPECTIVE] # 12, 1 CardiacSynchTechnique
(2001,1010) CS [TRIGGERED] # 10, 1 Unknown Tag & Data
(0018,1060) DS [300] # 4, 1 TriggerTime
(0018,9085) CS [VCG] # 4, 1 CardiacSignalSource
To deal with this, dcm2niix will not treat TriggerTime as a cardiac phase if the Acquisition Contrast (0008,9209) tag reports PERFUSION. This dataset demonstrates that each ASL phase is assigned a unique trigger time, presumably reflecting the label delay.
dcm2niix will convert a Philips ASL DICOM series as a single 4D NIfTI image. The 3D volumes are concatenated based on the factors of (a) repeat number, (b) phase number, and (c) whether the volume was a control or included a label. To analyze the data (e.g. with FSL's BASIL, you will need to specify the order of these factors.
- PhaseNumber (2001,1008) distinguishes phase number, as does TriggerTime (0018,1060).
- MRImageLabelType (2005,1429) distinguishes control from label images.
- MRImageDynamicScanBeginTime (2005,10a0) and TemporalPositionIdentifier (0020,0100) are identical for all Control/Label pairs and all phases, so they distinguishes the repeat.
For enhanced DICOMs, the Dimension Index Values (0020,9157) tag can distinguish volume type (phase, control/label, repeat), but does not match the temporal order. Classic DICOMs do not report 0020,9157 and Philips often assigns instance number (0020,0013) randomly, with no set relationship to these factors.
dcm2niix (from version v1.0.20210819) will always stack Philips ASL volumes in the same order. Regardless of whether the DICOMs were saved in enhanced or classic order. The order attempts to order the volumes in temporal order, but users need to be aware that the Philips DICOM data do not provide sufficient information to determine whether control or label images were acquired first.
Here is a concrete example for the volume order generated by dcm2niix. Consider an ASL sequence with three repeats and two phases. The order of the twelve volumes will be:
| Volume | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Phase | 1 | 2 | 1 | 2 | 1 | 2 | 1 | 2 | 1 | 2 | 1 | 2 |
| Label | C | C | L | L | C | C | L | L | C | C | L | L |
| Repeat | 1 | 1 | 1 | 1 | 2 | 2 | 2 | 2 | 3 | 3 | 3 | 3 |
The code and images are covered by the 2-clause BSD license.
- 5-August-2021 Initial public release
- 20-August-2021 Estimated temporal order
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.
- dcm2niix's handling of these files is described here.