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[ENH] Bep 005: Arterial Spin Labeling (#669)
* [ENH] Bep 005: Arterial Spin Labeling (#652) Co-authored-by: Patricia Clement <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Julia Guiomar Niso Galán <[email protected]> Co-authored-by: Remi Gau <[email protected]> * Update table errors * correction for table issues 'common metadata for PCASL/PASL' * correction latin phrases * Corrections tables * correction tables Cases * added link pepolar * deleted 'don't discriminate between types of labeling based on comment Thijs Van Osch * Moved MagneticFieldStrenght asl requirement to common * removed scaling factor info based on comment gllmflndn Removed: all ancillary scaling factors should be taken into account in the conversion to BIDS, which is why BIDS does not provide a separate scaling factor field other than the NIfTI header. * added MRAcquisitionType added in the common - sequence specifics table Reason: for ASL, defining 2D and 3D is required. This used to be added in the PulseSequenceType field, but this should stay a free text field. Therefore, the MRAcquisitionType field is added (based on DicomTag). * removed PulseSequenceType from the ASL part The 2D/3D information needed for ASL, is now moved to the new MRAcquisitionType field. * added required common fields sentence Some Common fields are required for ASL. To stress this out, we added a sentence for the *_as.json and the *_m0scan.json. * adaptation requirements for m0scan.json * adapted requirement level common fields for m0scan * update sentence required common fields for asl.json * Update common field EchoTime * Removed EchoTime from ASL-table * update FlipAngle in common RF and Contrasts * remove FlipAngle from ASL fields * update Dependency table ASL for MRAcquisitionType * update SliceTiming in common fields * remove SliceTiming from ASL tables * added (FA) for FlipAngle * update common RF and Contrast for table check * LabelingPulseDuration and LabelingPulseInterval in ms instead of s * required common metadatafields update RepetitionTime or VolumeTiming to RepetitionTimePreparation * update flipangle for timeseries versus file collections * update echotime for timeseries * update timing table (fence) * update definition BackgroundSuppressionPulseTime * removed common metadata fields from asl table MagneticFieldStrenght, EchoTime, SliceTiming, VolumeTiming, RepetitionTime, FlipAngle, PulseSequenceType * update scaling of asl and m0 files - update scaling description for nifti files - created separate scaling section (to highlight this important quantification factor), and M0 section - moved scaling section and M0 section after aslcontext section * update broken link in EchoTime (Timing Parameters) * update broken link (2) EchoTime * Update broken links FlipAngle * LabelingType changed to ArterialSpinLabelingType - changed in fields - Changed in dependency table - Dependency table: additionally removed repetitiontime/volumetiming parts * Update dependency table based on new M0Type and M0Estimate fields * Update new M0 field strategy M0 field becomes M0Type, with addition field M0Estimate. Also corrected IntendedFor description in m0 specific fields * TEMPORARY: disable 'strict' docs build this allows the build to proceed despite broken links * changed fail_on_warning to true Intermediate solution to get BEP005 build untill the missing link is available * see previous commit * update bep005 with latest master + resolve conflict (#689) * [DOC] Auto-generate changelog entry for PR #677 * [ENH] BEP001 - New entities: inv & mt (#681) * add entity inv * add mt: * add MT specific metadata * Generate entity.md * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Stefan Appelhoff <[email protected]> * Update src/schema/entities.yaml Co-authored-by: Stefan Appelhoff <[email protected]> * table fix by @sappelhoff * Conditional requirement Co-authored-by: Stefan Appelhoff <[email protected]> * [ENH] BEP001 - Entity-linked file collections (#688) * Squashed commit of the following: commit 8e1ac5f Author: Stefan Appelhoff <[email protected]> Date: Fri Nov 27 11:09:24 2020 +0100 fix links and latin commit 27c9b41 Author: Stefan Appelhoff <[email protected]> Date: Fri Nov 27 10:03:51 2020 +0100 remove latin Co-authored-by: Chris Markiewicz <[email protected]> commit 7d87070 Author: Agah <[email protected]> Date: Mon Nov 23 08:46:47 2020 -0500 Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz <[email protected]> commit b137a9e Author: Agah <[email protected]> Date: Mon Nov 23 08:45:19 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> commit d7897b8 Author: Agah <[email protected]> Date: Mon Nov 23 08:44:40 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> commit 09e9d32 Author: Agah <[email protected]> Date: Mon Nov 23 08:44:15 2020 -0500 Commit suggestion Co-authored-by: Chris Markiewicz <[email protected]> commit 009a9ab Author: Agah Karakuzu <[email protected]> Date: Mon Nov 23 08:43:00 2020 -0500 Add file-collecitons appendix to the TOC commit 8f6c4df Author: Agah Karakuzu <[email protected]> Date: Mon Nov 23 08:41:13 2020 -0500 Address suggestion by @tsalo commit 45210a9 Author: Agah Karakuzu <[email protected]> Date: Wed Nov 11 14:32:20 2020 -0500 Wording commit 66ba5a5 Author: Agah Karakuzu <[email protected]> Date: Wed Nov 11 14:31:40 2020 -0500 RECOMMENDED --> MUST for adding an application def to the appdx commit 5611fac Author: Agah Karakuzu <[email protected]> Date: Wed Nov 11 14:29:21 2020 -0500 Improve the appendix commit 6d3bbea Author: Agah Karakuzu <[email protected]> Date: Mon Nov 2 16:12:04 2020 -0500 Address suggestions by @tsalo commit bcb0223 Author: Agah Karakuzu <[email protected]> Date: Tue Oct 27 21:37:26 2020 -0400 [ADD] Link to the appendix commit 44e760f Author: Agah Karakuzu <[email protected]> Date: Tue Oct 27 21:28:38 2020 -0400 [ADD] Appendix - File collections - For parametrically linked file collections commit 523b1c1 Author: Agah Karakuzu <[email protected]> Date: Tue Oct 27 21:27:52 2020 -0400 [ADD] Parametrically linked file collections - Description * ENH: Link to all BEP-001 entities * STY: Escape asterisk, adjust table widths * Add suggestions by @sappelhoff * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/02-common-principles.md Thank you @effigies! Co-authored-by: Chris Markiewicz <[email protected]> * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Agah Karakuzu <[email protected]> * [ENH] BEP001 - RepetitionTimeExcitation and RepetitionTimePreparation (#671) * [ENH] Improve TR definitions - Include RepetitionTimePreparation - Include RepetitionTimeExcitation - Add explanation on the former RepetitionTime field. * Typo * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * ENH: Allow for variable RTE/P * STY: Update table widths * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md * Change ref to DOI @Remi-Gau * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> * Update config.yml * Update readthedocs.yml Co-authored-by: bids-maintenance <[email protected]> Co-authored-by: Agah <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> * update required common fields for m0scan.json added EchoTime and FlipAngle in case LookLocker is true * update dependency table if PCASL : LabelingDuration is required if PCASL: LabelingDuration should not be filled in * update depedency table removed 'PASL' LAbelingDuration should not be filled in * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * update description aslcontext Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * update PCASLType and CASLType Co-authored-by: Chris Markiewicz <[email protected]> * updated required into REQUIRED for asl.json and m0scan.json (common fields * Added SummaryImages Added images: asl_pasl_boluscutoff_false.png asl_pasl_boluscutoff_true_q2tips.png asl_pasl_boluscutoff_true_quipssII.png asl_pcasl_labeling_pulses.png asl_pcasl_sequence.png * create Appendix 11 for ASL * Added asl_flowchart.png * added subtitles for linking from main specification * Added appendix link for control and label * added appendix for asl sequences in general * added appendix for (P)CASL * added appendix for PASL * added appendix for dependency table (flowcharts) * MNT: Add ASL appendix to TOC * TYPO: correct ASL appendix entry in tocwq * fix md style * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz <[email protected]> * update table RF and Contrast * update link Appendix XI to Appendix XI - ASL * corrected link to appendix for PASL * Update aslcontext cases Case 1: changed asl.json to asl.nii[.gz`] Removed: The optional deltam or cbf volumes should be stored and specified as derivative. Case 2: Removed: The optional cbf volumes should be stored and specified as derivative. * Added aslcontext.tsv cases this is moved from main spec bep005 to appendix XI - ASL * Update aslcontext cases - moved three cases to appendix XI - ASL - added link to appendix XI - added: Note that the raw images, including the m0scan, may also be used for quality control. * corrected subtitles cases * improve linebreaks in ASL appendix * fix VascularCrushingVENC link Based on comment of Stefan Appelhof, the Data Type for VascularChrushingVENC was fixed: [number][] or \[array][] of [numbers][] to [number][] or [array][] of [numbers][] * added single column requirement for aslcontext.tsv based on comment of Stefan Appelhof, the need for a single column was added in the introductory text for aslcontext.tsv, before the 3 cases. * Changed VascularCrushingVENC to VascularCrushingVenc * [SCHEMA] Add ASL to schema (#703) * Add ASL to schema files and regenerate entity table. * Fix style issue. * Add fmap-format m0scan to schema. * update M0Estimate fields Added 'Referring to the M0 of blood' * update LabelingDuration Added additional information for LabelingDuration * update labeling.jpg into *_asllabeling.jpg * Change labeling to asllabeling. (#709) * RF: Renumber ASL appendix to XII Co-authored-by: Henk Mutsaerts <[email protected]> Co-authored-by: Patricia Clement <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Julia Guiomar Niso Galán <[email protected]> Co-authored-by: Remi Gau <[email protected]> Co-authored-by: bids-maintenance <[email protected]> Co-authored-by: Agah <[email protected]> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: Taylor Salo <[email protected]>
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