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ExploreASL Change Log

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

ExploreASL v1.10.0

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 #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.

ExploreASL v1.9.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15
  • dcm2niix 20190902

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

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

ExploreASL v1.6.1

Bug Fixes

  • Issue #578 Fix incorrect path searching by providing error if no .json-file is inputted

ExploreASL v1.6.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Feature improvements (still backward compatible)

  • Issues #62, #266, #449: JSON i/o unify and use spm_jsonread and spm_jsonwrite for all operations
  • Issue #349: Improve screenprint of the current subjects/sessions/modules by xASL_Iteration
  • Issue #384: Add method to export image matrices as structured points in VTK format
  • Issue #523: Update ExploreASL_ImportConfig to work with JSONs and add alert for users
  • Issue #538: Function to user-replace label values in atlas NIfTI, written for the CICERO study
  • Issue #559: Add option x.MakeNIfTI4DICOM to create CBF optimized for DICOM creation/PACS export

Work in progress

BASIL

  • Issue #20: Data pre-processing prepared for BASIL
  • Issue #391: Add single-PLD model for BASIL

ASL-BIDS

  • Issues #290,#483,#484: Initial version of the ASL-BIDS import workflow
  • Issue #353: Correct conversion BIDS->Legacy for M0 with reversed PE direction
  • Issues #394,#514,#545: Improve modularity of the ASL-BIDS import module
  • Issue #411: Delete temporary folders in DICOM->BIDS conversion
  • Issue #421: Use ImageType DICOM field to detect scan order in GE in DICOM->BIDS import
  • Issue #426: Reading PLD from DICOM for GE in import to BIDS
  • Issue #479: ASL-BIDS import for Hadamard encoded FME sequences

DRO and QASPER

  • Issues #361,#443: Import and import test of DRO
  • Issues #467: Improve script to generate ASL-BIDS version of ASL DRO v2.2.0

Compilation/stand-alone version

Bug Fixes

  • Issue #184: Skip PVC in Population statistics, when this does not make sense for a given ROI
  • Issue #262: Improve GZIP on windows
  • Issue #341: Reduce extensive usage of ExploreASL CLI progress tracker
  • Issue #368: Fix problem with writing trailing zeros in real numbers in spm_jsonwrite
  • Issue #387: Remove graphical waitbar interface from xASL_im_ResampleLinearFair
  • Issue #415: xASL_Copy: Allow recursive copying of directories
  • Issue #418: Verifies the SliceTiming parameter if timing difference is consistent between slices
  • Issue #424,#454: Remove string and contains functions to ensure Matlab compatibility for R2016
  • Issue #430: Fix xASL_adm_ReplaceSymbols crash when trying to replace sub-strings in PhoenixProtocol field
  • Issues #433,#474,#542: Splitting of ASL and M0 - fix on rerun, split metadata, backup aslcontext.tsv
  • Issue #451: Clean unused code and cleaned the development directory
  • Issue #466: Warning if the equal sign is used in JSON files instead of colon
  • Issue #475: Fix error with studies that have a special character in their name
  • Issue #477: Change vascular territory atlases file extensions to .nii.gz
  • Issue #496: Fixed session numbers in population module
  • Issue #502: Fix smoothing of 4D NIfTIs
  • Issue #505: Allow Token Aliases in import to be row vectors in import
  • Issue #518: ExploreASL logo and verbose overview shown only once in a single pipeline run
  • Issue #520: Stop import workflow from creating Population folder in root directory
  • Issue #543: Minor fix of xASL_num2str behavior
  • Issue #563: Minor design fix for ExploreASL dataset initialization

Documentation

  • Issues #403,#423,#457: Improved inline comments and headers
  • Issue #452: Provide descriptions of available atlas options
  • Issue #463: Remove remaining markdown file to a separate Documentation repository
  • Issues #486,#489: Introduce document templates for GitHub QC Workflow
  • Issue #499: Make heading in documentation work in dark mode as well
  • Issue #515: Added tutorials to documentation
  • Issue #536: Create a first version of the QC walkthrough document in markdown

Testing

  • Issue #156: Make internal error messages more specific by providing subject information
  • Issue #352: Improve parsing of errors and warnings from log files
  • Issue #395,#416: Improve testing of BIDS import
  • Issue #517: Improve unit testing scripts
  • Issue #529: TestDataSet is in BIDS derivatives format
  • Issue #570: Release testing and minor documentation improvements

ExploreASL v1.5.1

Bug Fixes

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

ExploreASL v1.5.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Feature improvements (still backward compatible)

  • Issue #39: Create PV-corrected GM & WM CBF maps in native space
  • Issue #56,#410: Add Mindboggle atlas to ExploreASL and restructure general atlas access in population module
  • Issue #283: xASL_stat_GetROIstatistics provide more feedback on missing images
  • Issue #299: Move CustomScripts with study-specific scripts to a separate repository
  • Issue #302: Remove server calls in CAT12 functions
  • Issue #313: Move GUI to a separate repository
  • Issue #351: T2 and T1c files are now also aligned to the T1w and outputted to standard space
  • Issue #354: Added an option x.DummyScanPositionInASL4D that removes marked dummy scans when splitting ASL to ASL+M0+dummy
  • Issues #356,#396,#397: Internally restructure SliceTime allowing ExploreASL now to work with multi-band 2D EPI as well or any other SliceTime order

Work in progress

ASL-BIDS

  • Issues #163,#189,#357,#373: Conversion from DICOM to BIDS
  • Issues #334,#382: Import of PAR-REC to BIDS
  • Issue #343: Add separate M0 option to mTrial import

Compilation/stand-alone version

  • Issue #335: All input arguments can be passed in the deployed mode
  • Issue #380: Enable advanced input parsing for xASL compiled

Bug Fixes

  • Issue #228: Fix CAT12 warnings with non-existent field cm
  • Issue #272: Fix errors in JSON import of ASL sidecars
  • Issues #273,#285,#291,#363: Minor fixes in input parameter administration
  • Issues #276,#280,#288,#329,#400: Fix error in reading TSV files with unclear number of columns
  • Issue #282: Population module is run serially in otherwise parallel mode
  • Issue #292: xASL_qc_SortBySpatialCoV now use all subjects without skipping
  • Issue #305: xASL_adm_UnixPath: bug with Windows+WSL
  • Issues #306,#378: Fix JSON reading with 'i' interpreted as a complex number
  • Issue #309: Fix non-linear registration of T1w to standard space with too high T1w values
  • Issue #312: xASL_stat_GetROIstatistics fix skipping of actual ROI extraction
  • Issue #325: xASL_adm_CleanUpBeforeRerun delete files correctly
  • Issue #339: Fix JSON reading of special characters
  • Issue #399: Fix special characters in Windows filenames
  • Issue #405: Fix range-check error in Background Suppression timing calculation
  • Issue #406: Fix xASL_stat_MedianNan for all-NaN input
  • Issues #408,#409: Skip missing fields in CAT during reports in compiled ExploreASL

Documentation

  • Issue #7: Create README files in subfolders and added to interactive documentation
  • Issues #279, #345: Move documentation to a separate repository
  • Issues #300,#318: Improve ExploreASL tutorial
  • Issue #355: Documentation improvements regarding input parameters

Testing

  • Issues #193,#350,#398: Testing DICOM to BIDS conversion against a reference
  • Issue #294: Implement initial unit testing framework
  • Issue #326: Parse warnings/errors from all log in all subdirectories
  • Issue #369: Unit testing of xASL_test_getLogContent
  • Issues #371,#376,#404: Testing script for the DICOM->BIDS->Legacy conversion and processing

ExploreASL v1.4.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Feature improvements (still backward compatible)

  • Issue #20 Implement BASIL -> changed order quantification/masking, and always save resampled PWI4D for quantification, facilitating BASIL
  • Issue #35 Calculation background suppression efficiency for pseudo-M0 -> in case of missing separate M0 images but still using background suppressed mean control as pseudo-M0, a single correction value (3D) or slice-wise correction value (2D) are applied to the pseudo-M0 image/slices
  • Issue #131 ExploreASL_GUI beta-testing enhancements set 1 -> Aesthetic improvements in certain modules, fixed incorrect removal of Philips-related json-sidecar fields in DCM2BIDS / Import module. Correction of ASL image flickering bug and ability for the user to subset without having to reload the data. Added ability to clarify data type of variables without the need to reload data. Added auto-select / auto-complete functionality in the ParmsMaker module as soon as the user indicates an analysis directory (i.e auto-completion of SliceReadoutTime for pCASL)
  • Issue #166 Update ADNI import in ExploreASL_Import
  • Issue #179 Finish creation average maps for CICERO -> improvements xASL_wrp_CreatePopulationTemplates
  • Issue #190 Hammers atlas option CAT12 -> restored the original Hammers atlas option for a colleague (note it's license though!)
  • Issue #225 Create DataPar option for running SPM12 longitudinal registration
  • Issue #241 Add warning when loading data without x output structure
  • Issue #243 Shorten SPM initialization time -> removed configuration loading of unused toolboxes (check if the SPM DICOM import module is still needed)

Work in progress

ASL-BIDS

  • Issue #193 Comparing BIDS folders (for testing purpose)
  • Issue #226 Add new DICOM tags to DCMTK import

Bug Fixes

  • Issue #191 WMH warning when no FLAIR analyzed -> this warning is now removed if no FLAIR was present in the data
  • Issue #248 Temporary fix native space processing -> in Population module
  • Issue #252 Population modules analysis masks - minor errors
  • Issue #267 Error in reading JSONs from EPAD

Documentation

  • Issue #196 All contributors -> all contributors are now automatically added to the main README.md
  • Issue #217 Documentation improvements
  • Issue #219 Add user to documentation

ExploreASL v1.3.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Feature improvements (still backward compatible)

  • Issue #59: Assign "weights" to status files, allowing the external Python ExploreASL GUI to provide a better estimate of the progress
  • Issue #71 Remove custom lesions (Lesion\_(FLAIR|T1)\_\\d\\.nii) from WMH_SEGM.nii
  • Issue #76: Improve functionality of ExploreASL through Command Line Interface (CLI), i.e. without using the Graphical User Interface (GUI) of Matlab
  • Issue #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 succesfully 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
  • Issue #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

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

ASL-BIDS

  • Issue #82 Avoid 4D files with nT==1, which is not allowed in the BIDS validator

Compilation/stand-alone version

  • Issue #88 xASL_SysMove error in Windows when a path includes whitespaces ' '

Bug Fixes

  • Issue #85 Improvement ApplyQuantification
  • Issue #99 Improve loading of metadata (xASL_str2num & xASL_init_LoadMetaData)
  • Issue #105 In case of missing data, fill x.S.SUBJECTID and S.DAT data for the last subject/session
  • Issue #119 Create status file for last subject, if it's processing is skipped
  • Issue #120 xASL_im_CreateAnalysisMask in native space mode when in parallel execution
  • Issue #138 Fix structure TestDataJSON & its JSON files
  • Issue #139 Ensure that x fields are not case sensitive, by e.g. replacing strcmp by strcmpi
  • Issue #141 Solve conflicts between develop and master, these were minor edits that weren't implemented in develop yet
  • Issue #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)
  • Issue #148 Syncing the ROI/lesion processing of T1w & FLAIR
  • Issue #151 Minor bugfixes for TopUp
  • Issue #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

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

Testing

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

ExploreASL v1.2.2

Bug Fixes

  • Issue #119 xASL_wrp_LinearReg_T1w2MNI.m: ROI .nii files correctly aligned with T1

ExploreASL v1.2.1

Bug Fixes

  • xASL_qc_TestExploreASL: Remove locked folders if rerun
  • Issue #90 xASL_io_Nifti2Im: manage the detection of odd scaling
  • Issue #93 xASL_SysMove: diz illegal symbols Windows
  • Issue #102 xASL_wrp_CreatePopulationTemplates: minor bugfix
  • Issue #104 Fix creation ResultsTable for TestCases (also #86)
  • Issue #114 Acquiring Matlab version doesn't crash anymore in deployed mode
  • Issue #115 Fixing NaNs problem in M0 mask computation

  • Issue #118 xASL_adm_GzipAllFiles doesn't crash anymore in Windows

  • Issue #116 ExploreASL testing fixes:

    • Edit header of saved .tsv-file
    • Cosmetic changes\nUnzip before SPM
    • Clear variables before loading .mat
    • Replace spaces in headers with underscores (which happened automatically apparently upon saving)
    • Remove SPM cellstring
  • Issue #96 Fix order of magnitude in JSON sidecars
  • Issue #109 No warning if SliceReadoutTime not provided in DataPar
  • Issue #110 xASL_bids_parms2BIDS.m now deals correctly with vectors and SliceReadoutTime = 'shortestTR': created function for this: xASL_quant_SliceReadoutTime_Shortest_TR

ExploreASL v1.2.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Major feature improvements (still backward compatible)

  • Add user flexibility for creating average maps, allowing flipping

  • Provide a lesion or ROI mask, to be used not only for cost function masking but also as standard space ROI for ROI-analysis This use is now easier, by simply adding Lesion_FLAIR_1.nii or Lesion_T1_2.nii etc, and visualization improved. These masks are now automatically created (where lesion can be any other ROI):

  • Intralesional

  • Perilesional, pGM+pWM
  • Hemisphere (ipsilateral to lesion)
  • Contralateral (i)
  • Contralateral (ii)

  • Contralateral (iii)

  • Option x.S.bMasking added, allowing specifying masking separately for:

  • bSusceptibilityMask

  • bVascularMask
  • subject-wise bGMMask (e.g. the pGM>0.7)

  • brainmasking when loading for lower memory usage

  • Affine registration improved & Discrete Cosine Transform (DCT) non-linear registration option added, including an option with partial volume correction built-in for improved DCT-based registration

Bug Fixes

  • Allow zipping in Unix-based OS without JavaVirtualMachine
  • Quantification issue with Philips scale slopes
  • DCTMK fix, import parameters
  • Use xASL_adm_UnixPath() for Unix system calls, for correct path usage (e.g. for spaces that need escaping)
  • Double escaping of backslashes in converting .m to .json for DataPar file - subject-regexp
  • Compilation path error
  • Correctly concatenate numbers when xASL_num2str
  • Improvements xASL_adm_LoadParms for converting parameters ASL flavors to BIDS/ExploreASL internally

Features

  • New startup option for starting ExploreASL, loading data, without processing data
  • Shortcut ExploreASL for ExploreASL_Master
  • Now we have xASL_csvWrite, xASL_csvRead, xASL_tsvRead, xASL_tsvWrite
  • xASL_io_Nifti2Im now detects erroneously extreme high scaling (potential import issue with Philips RescaleSlope) issues a warning and/or tries to fix automatically for FLAIR/T1w images

Work in progress

  • Docu Crawler for automatic documentation creation
  • ExploreASL_Import for different ASL flavors
  • BIDS implementation import

Documentation

  • create new prefix for visualization functions (xASL_vis\_\* instead of xASL_im\_\*)
  • revamp quantification functions for better headers, comments etc

ExploreASL v1.1.3

Bug Fixes

  • hotfix minor bug in running the import using DCMTK without the Matlab Image Processing Toolbox #30

ExploreASL v1.1.2

Bug Fixes

  • hotfix minor bug in loading NIfTIs containing lesion masks in CAT12 #28

ExploreASL v1.1.1

Bug Fixes

  • hotfix minor bug in creating participants.tsv #23

ExploreASL v1.1.0

Versions included software

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

  • SPM12 7219
  • CAT12 r1615
  • LST 2.0.15

Bug Fixes

  • Bug fixes and overall code improvements related to the BIDS import workflow (#11)
  • Registration with poor CBF contrast will not issue an error anymore but correctly switch to control-T1w registration only (#17)
  • Unexisting x.Sequence field fixed, now an appropriate warning is issued and this field is defined automatically by xASL_adm_DefineASLSequence.m (#16)

Features

  • Quantification can now be fully disabled by: x.ApplyQuantification = [0 0 0 0 0]; (#14)
  • Insert option to disable M0-ASL registration (#13)
  • Update of CAT (Computational Anatomy Toolbox) from version 12.5 to 12.7 (#2)

Work in progress

  • Minor improvements of custom scripts for BBB-ASL and BIDS (#8)
  • Minor improvements regarding unit testing of ExploreASL (#10)
  • Additional warnings for ExploreASL users (#12)

Documentation

  • Recent changes include the improvement of the documentation within the ExploreASL structure using markdown files and the introduction of a new documentation repository (#7)
  • Some function headers were added for increased understandability (#19). These can be viewed in Matlab by: help ExploreASL_Master where you can replace ExploreASL_Master by the actual function name

ExploreASL v1.0.0

This is the first release version.

Versions included software

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

  • SPM12 7219
  • CAT12 r1363
  • LST 2.0.15