ExploreASL/ExploreASL: ExploreASL v1.8.0
Bibliographic record
Abstract
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
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.013 |
| Meta-epidemiology (narrow) | 0.004 | 0.003 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.007 | 0.008 |
| Open science | 0.006 | 0.007 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.408 | 0.459 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".