ExploreASL/ExploreASL: ExploreASL v1.3.0

ExploreASL v1.3.0 Feature improvements (still backward compatible)

• #59: Assign "weights" to status files, allowing the external Python ExploreASL GUI to provide a better estimate of the progress
• #71 Remove custom lesions (Lesion\_(FLAIR|T1)\_\\d\\.nii) from WMH_SEGM.nii
• #76: Improve functionality of ExploreASL through Command Line Interface (CLI), i.e. without using the Graphical User Interface (GUI) of Matlab
• #123 Create status files also for skipped processing parts: this is mainly the case for running the structural module without a FLAIR scan. Having all status files helps third-party tools such as the Python ExploreASL GUI to know that processing has successfully completed (duplicate issues #137 and #129)
• The same was done for the ASL realignment status file, in case realignment is skipped for a 3D scan
• #145: Improve .nii(.gz) management in xASL_spm_deformations: allow either .nii or .nii.gz as input, treat them equally, and when .nii.gz is provided as output path, zip the resulting deformed image

Work in progress

• #32 Docker integration
• #55 ExploreASL GUI, written in Python
• #106 xASL_im_SplitImageLabels: Allow splitting labels, and warping them to standard space. This is part of continuous development on creating average flow territory templates and figures.
• #162 Remove bNativeSpaceProcessing from TestDataSet for now, return this when bNativeSpaceProcess is made more modular

ASL-BIDS

• #82 Avoid 4D files with nT==1, which is not allowed in the BIDS validator ### Compilation/stand-alone version
• #88 xASL_SysMove error in Windows when a path includes whitespaces ' '

Bug Fixes

• #85 Improvement ApplyQuantification
• #99 Improve loading of metadata (xASL_str2num & xASL_init_LoadMetaData)
• #105 In case of missing data, fill x.S.SUBJECTID and S.DAT data for the last subject/session
• #119 Create status file for last subject, if it's processing is skipped
• #120 xASL_im_CreateAnalysisMask in native space mode when in parallel execution
• #138 Fix structure TestDataJSON & its JSON files
• #139 Ensure that x fields are not case sensitive, by e.g. replacing strcmp by strcmpi
• #141 Solve conflicts between develop and master, these were minor edits that weren't implemented in develop yet
• #143 ensure that VBA masks are also created for a 3D spiral sequence (this was not created yet as the susceptibility masks were missing for this sequence)
• #148 Syncing the ROI/lesion processing of T1w & FLAIR
• #151 Minor bugfixes for TopUp
• #177 Fix xASL_adm_UnzipNifti & xASL_io_SaveNifti when path is incomplete
• • Skip warnings for small populations (in the start of xASL_module_Population)
• Fix regular expression in xASL_init_LoadMetaData
• iRow counting fix in xASL_bids_Add2ParticipantsTSV

Documentation 7 Documentation/revamp xASL_im_ClipExtremes 159 Ensure that all sequence notations use underscores instead of whitespace, e.g. 3D_spiral instead of 3D spiral Testing

• #86 xASL_qc_TestExploreASL: improve Table creation
• #112 Save Tanimoto Coefficient (i.e. a fuzzy overlap/Dice score) of the final ASL-T1w registration
• #128 Improved one internal test dataset
• #130 xASL_qc_TestExploreASL: Complete functionality by allowing Windows parallelization & testing the Windows ExploreASL compilation. Also added unit testing framework in the same issue.