Master issue for fixing processing things for flavors.

Identified the problem and created an issue:

• Philips_PASL_2DEPI_5.4.1.0_ADNI3_006_S_6681_1 - Crashes CBF quantification - Quantify single-PLD PASL without bolusCutOff #794
• Siemens_PASL_3DGRASE_E11_1 - MOSAIC not read correctly (import error), and then the pipeline crashes. Import does not work with all MOSAICs #407
• Philips_PASL_2DEPI_5.4.0.2-LookLocker_1 - Pairwise subtraction not working, TC coeff not working Look-Locker motion correction #987
• Some flavors needs manual preparation Incorrect import testing #710
• -Siemens_PCASL_3DGRASE_VB17A_multiPLD_1 - BsupM0 correction does not work for multiPLD Bsup M0 correction for multi-TI #988
• SPM realign crashes for newer ADNI cases #877
• Motion correction bug & feature requested by Anouk Schrantee EPOD #1120

To be fixed (no issue exist yet):

• Philips_PCASL_3DGRASE_5.1.7.2_1 - crashes ASL module because we accidentally put zeroed-out data to Flavors - need non-zeroed data from Henk
• We get the following warning (also when running older GE flavor release DV22.0): Warning: Field EchoTime in xASL structure has a value 0.0528, which is outside of the recommended range <0.5,500> ms.
• Philips_PCASL_3DGRASE_5.4.1.0_TopUp_1 - some issues running FSL - check again.
• Siemens_PCASL_3DGRASE_VB17A_TopUp_1
• Siemens_PASL_3DGRASE_VE11C_2 - Creates an image full of NaNs that later crashes the pipeline. Find out what is causing this empty image.
• Lot of warnings about mismatch in SliceTiming, SoftwareVersion etc. - check which one is correct and remove them from studyPar.json to minimize warnings.
• GE_PCASL_3Dspiral_DV25.0_1.5T_1: In the dcm2NII stage, this will issue a LabelingDuration conflict warning, and it then stores: "LabelingDuration":0.00145,. Both PostLabelDelay and InversionTime are detected but removed in our nii2BIDS.
• I got a warning about missing recommended field HEDversion, which is related to functional imaging only (hierarchy of behavioral events), not to ASL. So this should be removed. Philips_PCASL_2DEPI_5.1.7.2_BSupN_1

Fixed:

• Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1 - import doesn't work yet