Description

Required: insert bug description here

Tasks

• xASL_wrp_RegisterASL: Quick & dirty ASL->T1w registration improvement for TC<0.55
• xASL_adm_CleanUpBeforeRerun: Improve session handling for non-ASL modules
• xASL_adm_CreateFileReport: Facilitate running outside of ExploreASL modules
• xASL_im_SkullStrip: Add warning, potentially useful for debugging
• xASL_wrp_LinearReg_T1w2MNI: Bugfix when no other NIfTIs are found

Moved from #1233

• 1. When bRegistrationCBF is off, no need to create a VascularTemplate file; HENK: true, but if then no meanControl is found, we force bRegistrationCBF, so easier to always create a VascularTemplate file. It is deleted at the end.
• 2. What happens if x.modules.asl.bRegistrationContrast==0 but no mean_control exists? Should issue warning & skip registration HENK: we have this on line 388: we first try M0->T1w instead, if M0 also doesn't exist, we skip the registration. I added now to default bRegistrationCBF to true if this is the case.
• 3. if x.modules.asl.bRegistrationContrast == 0 but we only have a PWI or CBF image, do we default to x.modules.asl.bRegistrationContrast == 2? HENK: yes I added this now per (2).

How to test

Henk is rerunning the population mentioned in #1893 & will report how it works, but risk of the registration fix is small, it is just more conservative (we had a sCoV threshold already, but this can be wrong if the TC is too low, then the sCoV may not be correctly captured).

See these FACEHBI subjects:
Tra_qCBF_sub-15293275_2_ASL_1 -> misalignment because of vascular? just a 1 cm too low and to left
Tra_qCBF_sub-15350011_2_ASL_1 -> dimensionality flip/ vascular
Tra_qCBF_sub-15380711_2_ASL_1 -> dimensionality flip/ vascular
Tra_qCBF_sub-15380711_5_ASL_1 -> misalignment because of vascular? just a 1 cm too low and to left
Tra_qCBF_sub-16075332_2_ASL_1 -> dimensionality flip/ vascular
Tra_qCBF_sub-17103413_5_ASL_1 -> misalignment because of vascular? just a 1 cm too low and to left
Tra_qCBF_sub-17132877_2_ASL_1 -> misalignment because of vascular? just a 1 cm too low and to left
Tra_qCBF_sub-17178091_2_ASL_1 -> dimensionality flip/vascular
Tra_qCBF_sub-17288255_5_ASL_1 -> misalignment because of vascular? just a 1 cm too low
Tra_qCBF_sub-17411419_5_ASL_1 -> dimensionality flip/vascular
Tra_qCBF_sub-17534701_5_ASL_1 -> dimensionality flip/vascular
Tra_qCBF_sub-18328827_5_ASL_1 -> misalignment because of vascular? just a 1 cm too low

Good example (nice registration, CBF contrast): sub-16017046_2

Now, after this bugfix, only the following ASL images are misaligned:

dimensionality flip/ vascular
sub-15380711_2

slightly 1 cm
15380711_5
17103413_5
17132877_2
17411419_5
17534701_5

Release notes

Registration fix for vascular-appearing CBF maps