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Dummy volumes #748

Open HenkMutsaerts opened 3 years ago

HenkMutsaerts commented 3 years ago

Description

Dummy scans

If there are dummy scans inside the DICOMs/NIfTIs, they should be removed from the NIfTI. Then the NumberOfVolumesDiscardedByUser should be added with the number of volumes discarded.

(see also OASIS dataset: Siemens PASL 2D EPI)

QC steps (in BIDS2Legacy & in ASL module):

If scale slopes were already applied, this was a previous ExploreASL version.

_aslcontext.tsv should be adapted accordingly

Requirements

Optional: add feature requirements here

How to test

Optional: insert description about how to test the code changes here

Release notes

Required: summarize the changes for the release notes here

BeatrizPadrela commented 3 years ago

I was processing OASIS, and before the processing, I was already deleting the first volume (with the script to prepare the data before processing - CustomScripts), to keep the correct 104 volumes instead of 105 (this one extra is the dummy scan). However, during the ASL module, there's a check for this dummyscanposition, and it deletes again the dummy scan (103 volumes instead of 104):

image

So, either we remove the dummy scan before, or we just keep the dummy scan and add the field DummyScanPositionInASL4D. Because the SplitASL function receives an input called iDummy, xASL_io_SplitASL(inPath, iM0, iDummy), based on an x.modules.asl.dummy image

Just fyi