ExploreASL/ExploreASL: ExploreASL v1.8.0

ExploreASL v1.8.0 Versions included software

Versions included & used third-party tools (see /External/README_SPM.txt):

• SPM12 7219
• CAT12 r1615
• LST 2.0.15

• Release issue #805: xASL_bids_BIDS2Legacy (check for empty visits), ExploreASL_Master (update unit testing), xASL_stat_StdNan (update unit testing), xASL_qc_CreatePDF (minor change related to new PDF filename), xASL_imp_DCM2NII_Subject_SortASLVolumes (minor bugfix), xASL_imp_NII2BIDS (print user feedback for existing subjects/sessions), xASL_imp_Initialize (check scan tokens), xASL_wrp_Quantify & xASL_quant_SinglePLD & xASL_quant_Basil (return error if FSL is missing), xASL_adm_GetDeprecatedFields (add BASIL field), xASL_im_M0ErodeSmoothExtrapolate (use correct defaults for robustness, add warning)
• Issues #182, #721: Option to use template WM and contour for alignment QC
• Issue #187: Load NIfTI as UINT8 or INT16 if not floating point
• Issue #204: Development version of scripts for cluster testing of ExploreASL
• Issue #311: Generalize TSV writing behavior of ExploreASL
• Issue #412: Make sure that the regular expressions for files are case insensitive
• Issue #442: Added default T1-time values for different field-strengths than 3T
• Issue #566: Basic motion correction for Hadamard and multi-TE and multi-PLD
• Issue #569: Minor fix in setting up FSL, issuing a warning when FSL version<6, and testing bUseBasilQuantification in both a 2D and 3D ASL dataset
• Issue #574: Update unit tests regarding backwards compatibility
• Issues #575, #754, #757, #770: Simplification/revamp of some scripts that check image flips and report on them
• Issue #595: Save NIfTI as UINT8 or INT16 if the values are integers
• Issue #611: Adapt participants.tsv to BIDS format
• Issue #639: New BIDS fields defined for TimeEncoded and automatic import of TimeEncoded data from FME
• Issue #680: xASL_im_Lesion2Mask: Separate masks in 4D NIfTI if they are not mutually exclusive
• Issue #683: Modularize data loading of ExploreASL
• Issue #687: Update reference values for pipeline testing
• Issue #690: Improved unit testing
• Issue #696: Run data compression after processing pipeline (not a part of the population module anymore)
• Issue #700: DCMTK-based DICOM reading compiled for MacOS using static libraries
• Issue #717: The ExploreASL x struct and with that some of the ExploreASL settings were moved to dedicated fields, for backwards compatibility a table was created and automated workflows were implemented
• Issue #746: Save ExploreASL version in both BIDS and legacy-derivatives imported data
• Issue #778: Optimize import workflow for code simplification and robustness
• Issue #790: Import ASL ordering by SeriesNumber
• Issue #796: BIDS import runs without ASL scans

• Bug #257: Slight revamp of xASL_wrp_CreateBiasfield
• Bug #565: Improved behavior of xASL_adm_DeleteFileList, which now understands if the same file is tried to delete twice (e.g., in the case of symbolic links)
• Bug #692: Fix minor error in xASL_fsl_TopUp
• Bug #707: Improve ExploreASL warnings for discontinued input behavior
• Bug #713: Fixing bugs originated from commits in #683 and #595
• Bug #725: Printf CBF results in TSV even if first ASL session ASL_1 is missing
• Bug #731: Print correct units for sCoV
• Bug #732: Improve overall subject/visit import behavior for both anatomical and perfusion files
• Bug #739: Try to automatically derive Manufacturer if missing in DICOM
• Bug #758: Fix bug related to data loading
• Bug #761: Stop pipeline from crashing for empty NIfTI files
• Bug #762: Fix TSV tables: default missing numbers or lists to n/a for now, and use '_' for placeholder elements
• Bug #769: Fix data loading of processed datasets
• Bug #774: Correctly manage zipping when moving identical files
• Bug #784: Accepting M0Type in studyPar in BIDS form for DCM->BIDS conversion
• Bug #806: If each slice has a separate scale slope but these are identical, this shouldn't report a warning
• Bug #808: Import submodules for each run which is being converted include logging feature as well as user feedback now
• Bug #810: Correctly convert multi-session BIDS2Legacy even if not all subjects have multiple sessions
• Bug #818: Prevent pipeline crashes for FSL/BASIL features where FSL directory can not be found

• Issue #702: Move discontinued code to a dedicated directory
• Issue #714: Minor clean-up cat_wmh_miccai2017.nii
• Issue #787: Move import & processing checks to the master script