ExploreASL v1.11.0

Versions included software

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

• SPM12 7219
• CAT12 r1615
• LST 2.0.15
• dcm2niix 20220720

Feature improvements

• Release issue #1423: New release.
• Features #1002, #1214, #1301, #1341, #1387, #1447, #1458, #1469, #1471: Multi-PLD quantification with BASIL and FABBER.
• Features #1128, #1300, #1367: Allow direct import of NIfTIs.
• Features #1311, #1348, #1419: Use Matlab functions instead of SPM for I/O of JSON files.
• Features #1396, #1408, #1411, #1449, #1468: Multi-TE time-encoded DEBBIE sequence quantification.

Bug fixes

• Bugs #577, #684, #1330, #1424, #1431: Fix issue with subject number in population filenames and allow sessions 10 and higher.
• Bug #1062: Fix TotalAcquiredPairs calculation with dummy scans for M0 splitting.
• Bug #1178: Fix symbol interpretation in longitudinal registration.
• Bug #1287: Fixed site-biasfield correction for more than 3 sites.
• Bugs #1288, #1290, #1308, #1318, #1393, #1405, #1435: Correct import of DCM2BIDS and BIDS2Legacy with duplicate anatomical scans, missing scans, improve message formatting.
• Bugs #1294, #1331, #1392, #1444: Fix import of GE and Siemens scans.
• Bug #1295: Save temporary CSV with WMH counts to subject folder and not population folder.
• Bug #1327: Fix WM maps conversion to native space.
• Bug #1338, #1453: Fix an incorrect path and crashes for NonCommercial atlases for CAT12.
• Bug #1361: if a single subject crashes the bids2legacy conversion, this won't crash other subjects anymore.
• Bug #1376: Fix bug xASL_bids_Add2ParticipantsTSV.
• Bug #1415: Correct import of PE-polar directions for M0.
• Bug #1481: Provide default T1-blood when hematocrit values are missing.

Optimization

• Issue #1120: Save motion parameters before and after spike removal.
• Issues #1320, #1334: Avoid additional zipping of BIDS and Legacy data after import.
• Issues #1270, #1326, #1356: Flavor-import testing allows to turn of certain dataset and other optimizations.
• Issue #1375: Add an option for absolute threshold on motion spike removal.
• Issues #1388, #1397: Optimizing token use in import in sourcestructure.json.

Documentation

• Issues #1336, #1381, #1403: Fix issue in citation.cff for Zenodo release.

Other improvements

• Issues #57, #89, #121, #222, #224, #229, #328, #413, #473, #507, #533, #541, #561, #751, #984, #991, #1018, #1034, #1048, #1052, #1057, #1072, #1158, #1181, #1194, #1208, #1209, #1230, #1268, #1299, #1344, #1402, #1417, #1455: Duplicit and review issues.
• Issues #508, #1171, #1437: Fix Singularity and Docker deployment.
• Issues #989, #1204, #1239: Add multi-PLD Siemens XA31 flavor.
• Issues #1247, #1477, #1484: Standardized Testing Script Results with proper results saving.
• Issues #1315, #1428: Add SequenceName tag to DCMTK reader.
• Issues #1319, #1366: Add Philips Look-Locker flavor.
• Issue #1324: Make ExploreASL and related code work on Apple Silicon.
• Issues #1362, #1407, #1451: Add Siemens multi-TE time-encoded DEBBIE flavor.
• Issue #1372: Add Matlab version check to the ExploreASL start-up
• Issue #1395: Calculate Siemens labeling duration from NumRFBlocks.

ExploreASL v1.10.1

Versions included software

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

• SPM12 7219
• CAT12 r1615
• LST 2.0.15
• dcm2niix 20220720

Hot fixes

• Bug #1276: Fix too time-demanding BIDS2Legacy conversion

Versions included software

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

• SPM12 7219
• CAT12 r1615
• LST 2.0.15
• dcm2niix 20220720

Feature improvements

• Release issue #1235: New release.
• Feature #435: Update dcm2nii to version 20220720.
• Feature #844: PVC maps calculated in native space are transformed to MNI space.
• Features #927, #1046, #1055, #1059, #1167, #1218: DEBBIE sequence -- Hadamard multi-TE ASL - basic import and processing.
• Feature #1011: Add Desikan-Killiany atlas.
• Features #1115, #1044: Revamped Import. BIDS2Legacy conversion is now done as first step of the processing module.
• Feature #1129: StudyPar supports multi-parameter definitions for import of multi-sequence datasets.
• Feature #1197: Allow configuring the image contrast for statistics in dataPar.json.
• Feature #1242: Correctly report errors in sourceStructure.json during import.

Bug fixes

• Bugs #685, #1182: Fix issue with atlas names.
• Bug #1068: Fix errors in susceptibility mask in xASL_im_CreateAnalysisMask.
• Bugs #1079, #1161, #1162, #1253: General bugfixing ExploreASL.
• Bug #1111: Disable M0 processing when M0 not present.
• Bug #1117: Fix Spatial CoV sorting of ASL images.
• Bug #1123: Avoid loading ExploreASL-related folder log as subject.
• Bug #1138: Fix subject directory name parsing for M0.
• Bug #1140: Handles an incorrect number of delimiters per line in TSV/CSV/DSV files loaded by spm_load.
• Bug #1164: Fix a bug in xASL_adm_GzipAllFiles.
• Bug #1187: Minor fix in xASL_csvWrite.
• Bug #1254: Minor fix of Philips scaling.
• Bugs #1256, #1271: Fix import, especially of FME and MacOS file-related issues.
• Bug #1259: Fix native space analysis.
• Bug #1262: Minor fix in Flavor-test script.

Optimization

• Issue #390: Create directories for QC only when writing the files in them.
• Issue #823: Cleaned unused functions in the Development folder.
• Issue #995: xASL_num2str always outputs a row vector.
• Issue #1040: Reorganize file structure of the code.
• Issue #1050: Move final zipping inside population module to avoid parallel execution.
• Issue #1105: Fixes input parameter checking at multiple locations and optimized internal variables.
• Issue #1159: Improve spm_jsonread warnings and print file path.

Documentation

• Issue #1075: Improve and restructure documentation.
• Issue #1149: Move dataParTemplates to online Documentation.
• Issue #1212: Improve explanation of studyPar.json and dataPar.json.
• Issue #1222: Added a new email to readme exploreasl.lab@gmail.com.

Other improvements

• Issue #1098: Skip requirement of BIDS quantification parameters when quantification not user accoridng to x.modules.asl.ApplyQuantification.
• Issue #1108: Simplify README.md and add CFF citation of ExploreASL.
• Issue #1112: Improve code comments in hematocrit correction.
• Issue #1118: Improve FEAST quantification warnings.
• Issue #1121: TestDataSet now contains BIDS rawdata only and no derivatives.
• Issue #1124: Allow basic background-suppression correction for M0 in multi-PLD.
• Issue #1134: Simplify script for version file reading.
• Issue #1136: Improved error output for ASLContext not matching with NIfTI dimensions.
• Issue #1142, #1153: Ignores JSON files or subdirectories in the root-directory input path.
• Issue #1201: Added GE RX28 flavor.

Versions included software

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

• SPM12 7219
• CAT12 r1615
• LST 2.0.15

Feature improvements

• Release issue #1015: New release.
• Feature #567: Adapt decoding and subtraction to Hadamard data.
• Feature #640: Calculate PWI image with Hadamard decoding.
• Features #759, #1014, #1021: Adapt ExploreASL pipeline to multi-PLD data.
• Features #799, #930, #945, #1017: Make import a full module.
• Feature #827: xASL_module_Population now does not start when ExploreASL is called in parallelization mode.
• Feature #845: New xASL_system function for all command line calls.
• Feature #907: Add WSL2 compatibility for FSL.
• Feature #911: Revamp initialization structure of xASL_module_ASL to restore a correct order of all steps.
• Feature #925: LabEff and T1blood defaults set for PASL at 7T according to Ivanov, Neuroimage, 2017.
• Feature #963: Clean the Hadamard decoding code. Add decoding matrix for Philips.
• Feature #975: Implement import of GE eASL sequence.

Bug fixes

• Bug #712: NIfTI comparison with regard to data types.
• Bug #848: Improve repetition-time field checks and add a user warning.
• Bug #853: Update longitudinal registration.
• Bug #868: Add fallback values for xASL_im_CreateAnalysisMask.
• Bug #873: Avoid spurious double registration of ASL to T1w.
• Bug #891: FSL TopUp configuration file was missing.
• Bug #892: Detect and remove pre-existing toolbox paths that might conflict with toolboxes included in ExploreASL.
• Bug #893: xASL_spm_admin crashed with cell input.
• Bug #909: Potentially too strict M0 masking.
• Bug #923: Improve import modularity and BIDS format of subject IDs.
• Bug #929: Import module crashes if no files were found.
• Bug #936: Fix rerun issues within import module.
• Bug #938: dcm2niix handling done in one place and corrected for PAR/REC.
• Bug #948: Update x.SUBJECT/S and x.overview for subjects with illegal characters.
• Bug #952: Backward compatible reading of PVC processing parameters.
• Bug #956: Fix input format of PVCNativeSpaceKernel.
• Bug #959: Remove EchoNumber and TimeEncodedEchoTimes fields from BIDS and optimized Hadamard import and initialization.
• Bug #978: BASIL for multi-PLD, Look-Locker, and Hadamard. Correct BASIL configuration. Output ATT maps.
• Bug #979: Fix x structure clean-up between import and processing.
• Bugs #980 & #982: Split ASLContext.tsv when splitting ASL and M0.
• Bug #1025: Correct NEX in GE eASL to account for the number of Hadamard phases. Correct GE scalings.

Optimization

• Issue #801: Remove warnings about default values in import.
• Issue #834: Flavor testing script for the up-to-date flavor database with new reference datasets.
• Issue #850: Improve resample and realign methods by adding parameter & field checks.
• Issue #855: Add unit tests for basic ExploreASL/SPM routines.
• Issue #860: Handle multiple anatomical files exported by DCM2NIIX.
• Issues #864, #1023: Improve user feedback for unit testing and initialization.
• Issue #874: Default import does not do defacing.
• Issues #888 & #902: Stop using Distributed computing and Parallel Toolboxes and parfor.
• Issue #913: Refactor xASL_im_ResampleLinearFair code.
• Issue #932: Remove legacy import.
• Issue #940: Improve the folder folder hierarchy check.
• Issue #947: Minor improvements of import master structure.
• Issue #971: Mean control image creation in a separate function.
• Issue #1033: Improve M0 processing to avoid masking-out intracranial signal, e.g., in M0 with strong biasfield

Other improvements

• Issue #836: Move cluster testing to CustomScripts.
• Issue #880: Improve ExploreASL unit testing with regard to directory changes.
• Issue #881: Philips Hadamard flavor added to Flavors and tested with import.
• Issue #942: Update unit tests for ASL-DRO.
• Issue #969: Improve atlas documentation.
• Issue #993: GitHub template change.
• Issues #1003 & #1007: Redesign of the ExploreASL README file.

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

Feature improvements

• 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 fixes

• 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

Other improvements

• 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

ExploreASL v1.7.0

Versions included software

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

• SPM12 7219
• CAT12 r1615
• LST 2.0.15

Feature improvements

• Issue #455: Automatically compare results of TestDataSets with a saved reference results
• Issues #480, #623, #649, #661: Restructure x: x.opts (input arguments and their derivatives), x.dir (directories), x.settings (mostly booleans for pipeline settings), x.dataset (dataset related fields), x.external, ...
• Issue #572: Restructure JSON handling during NiFTI to BIDS import
• Issue #580: Add parsing of Gold Standard Phantoms ASL-DRO
• Issues #588, #612: ExploreASL reads folders and automatically searches for sourceStructure, studyPar and dataPar JSON files
• Issue #600: Put participants.tsv to the derivatives folder during import to legacy ExploreASL format
• Issue #602: Remove option for cloning the NIfTI output after import as BIDS directory is a read-only archive
• Issue #603: Give ExploreASL version in JSON files after BIDS to Legacy conversion
• Issue #631: Remove repeated warnings
• Issue #632: Add comparison script for untouched NIfTI comparison
• Issue #643: bids.layout: avoid printing the same warning repetitively in case multiple scans in a data set have the same issue
• Issue #656: Improve warnings (data loading)

Bug fixes

• Issue #583: Proper testing of flavors using ExploreASL_Master
• Issue #584: Print the subject name depending on the existence of its definition in x.SUBJECT to avoid crashes for error reporting in the population module
• Issue #586: Avoid crashing xASL_adm_GetPopulationSessions if no sessions are found
• Issue #591: MultiTE import puts TE before PLD in the time series and corrects the JSON output
• Issue #618: Add session name to all M0Check and ASLCheck QC files in the Population folder
• Issue #620: xASL_adm_GzipAllFiles: Allow spaces in an input path for macOS/Linux
• Issue #625: Fix bug related to session format
• Issue #627: Remove a BIDS fiels and BIDS2Legacy should crash and show you why it crashed
• Issue #628: Fix parsing sessions and runs for converting rawdata to derivatives
• Issue #630: Move creation of population folder
• Issue #646: Improve BIDS warnings
• Issue #652: xASL_vis_CreateVisualFig: allow empty overlays
• Issue #659: xASL_stat_PrintStats: Fix visits bug (legacy format)
• Issue #655: xASL_adm_GetPopulationSessions gave incorrect warnings
• Issue #666: Warning when multiple dataPar*.json or studyPar*.json or sourcestructure*.json are present
• Issue #670: Fix warnings and behavior of ExploreASL_Initialize

Other improvements

• Issue #465: Add projects to acknowledgments
• Issue #615: Add change log to documentation
• Issue #637: Restyle ExploreASL change log

ExploreASL v1.6.2

Bug Fixes

• #589 Fix scaling issues in JSONs in TestDataSet/derivatives

ExploreASL v1.6.1

ExploreASL v1.6.0

ExploreASL v1.5.1

Bug Fixes

• #439 Fix population module error by correctly renaming MNI_Structural.* files