Description

Previously, xASL_module_Population worked sequence-specific, because of sequence-specific masking.
Now, the sequence-specific susceptibility masking is performed in xASL_module_ASL->xASL_wrp_CreateAnalysisMask,
and (xASL_module_Population->) xASL_im_CreateAnalysisMask -> xASL_im_CreateAnalysisMask_LegacySusceptibilityMasking performs some extra thresholding to create group masks, based on 2D EPI & 3D GRASE templates.

Requirements

• 1. Test the ASL module susceptibility mask creation.
  Using flavor Philips_PCASL_2DEPI_3.2.1.1_1, I tested the creation of the susceptibility mask inside the ASL module, which was a bit too lenient; around the susceptibility regions it was not correctly masked by the brainmask.
  This is not a problem, because eventually. several masks are combined, but it is cleaner to mask extra by the brain mask, because the default susceptibility mask IS a brainmask (e.g., for sequences without a susceptibility mask, such as 3D spiral).

The susceptibility mask BEFORE & AFTER population module masking are nearly identical.

Brainmask old susceptibility mask new susceptibility mask

• 2. This population-based part to create an analysis mask only runs when there are multiple subjects (e.g., more than 16). To change this, we will now ALWAYS create templates and a group analysis mask, even if we have n=1. But if n<5, we will issue a warning that this may not work well.

• 3. Check difference in masking only ASL module or also in population module:

Difference seems to be a small erosion around the original mask.

• 4. Test the output of xASL_im_CreateAnalysisMask_LegacySusceptibilityMasking for 2D EPI & 3D GRASE. Move this extra masking that it does to xASL_module_ASL
• 5. Remove xASL_im_CreateAnalysisMask - xASL_im_CreateAnalysisMask_LegacySusceptibilityMasking
• 6. Remove xASL_module_Population-xASL_adm_DefineASLSequence
• 7. xASL_stat_GetROIstatistics uses xASL_adm_DefineASLSequence on line 154, but is not using x.Q.sequence, x.Q.readout* or x.Q.vendor, so we can remove this here. Same for xASL_wrp_GetROIstatistics line 87 has xASL_adm_DefineASLSequence, which can be removed.

Release notes

Create sequence-specific mask in ASL module instead of the Population module.