Description

BASIL requires settings, currently defined in the Basil_ModelOptions.txt file, for ATT quantification. The Include macrovascular component setting is not included but should be to quantify ATT accurately.

Tasks

• Check if 'simple' masking helps speed-up BASIL processing
• Parameters are incorrectly added to basil_options and should be added to the command line calling basil
• Add dispersion parameter --disp=gamma at line 375, change code to [basiloptions xxx]
• Add arterial component parameter --inferart at line 364, change code to [basiloptions xxx]. Default is on for multi-PLD?
• Spatial regularlization is recommended, always turn on by default
• iaff=diff not needed as BASIL only accepts PWI and other steps are performed before PWI is obtained https://asl-docs.readthedocs.io/en/latest/basilcmd_examples.html?highlight=iaf%3Ddiff.
• -@ basil_options.txt should be --optfile basil_options.txt, also true for FABBER https://fabber-core.readthedocs.io/en/latest/running.html
• --save-model-fit is not an option in BASIL
• --allow-bad-voxels not an option in BASIL, also we don't do structural space analysis right?
• Check if datapar options exist for BASIL settings
• Add to documentation, at x.Q. etc.
• Jan check documentation changes,
• Jan recompile and publish documentation.
• Copy fblood to ABV map
• Check how CBF/ATT/ABV is copied to ASL_x folder from BASIL output folder - use the latest step. | Latest step is searched for, so all good |
• Fix here also Adding BASIL single-PLD quantification to the unit tests #558 Jan: Commits copied, testing will be done later.
• Fix here also Merge BASIL and FABBER calls #1181
• Merge BASIL and FABBER and call the function xASL_quant_FSL
• Make sure that FSL options for BASIL and FABBER are done the same way in xASL_sub_FSLOptions
• Fix FABBER call with the correct options and options file
• Delete previous BASIL/Fabber output -> here the output may be separate for calculating different maps (e.g., one may want to compute Tex twice, once with CBF and ATT maps from sequence A and once from sequence B)
• Add option (configurable in dataPar.json) to turn off deleting FSL input/output to xASL_quant_FSL.
• Check units and scalings for ABV.
• --output and --data for FABBER - provide as absolute path.
• For FABBER DEBBIE, we provide TIs (time from labeling to readout for PASL). Sometimes for PCASL , TIs are also provided instead of PLDs but TI=PLD+Tau. So I don't understand why we provide TI=PLD for FABBER for DEBBIE. Can @BeatrizPadrela and @amahroo explain that this is correct.
• Keep PWI4D

Release notes

Fix calling BASIL and FABBER.