Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[ENH] BEP001 - Entity-linked file collections #688

Merged
merged 10 commits into from
Dec 1, 2020
Merged

[ENH] BEP001 - Entity-linked file collections #688

merged 10 commits into from
Dec 1, 2020

Conversation

effigies
Copy link
Collaborator

@effigies effigies commented Dec 1, 2020

Trying again. I squashed #683 onto the latest master and pushed to bids-bep001/file-collections-redux so I didn't damage other history.

This replaces #668 and #683.

@effigies
Squashed commit of the following:
d8f3b2d 
commit 8e1ac5f
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 11:09:24 2020 +0100

    fix links and latin

commit 27c9b41
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 10:03:51 2020 +0100

    remove latin

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 7d87070
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:46:47 2020 -0500

    Update src/99-appendices/10-file-collections.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit b137a9e
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:45:19 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit d7897b8
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:40 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 09e9d32
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:15 2020 -0500

    Commit suggestion

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 009a9ab
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:43:00 2020 -0500

    Add file-collecitons appendix to the TOC

commit 8f6c4df
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:41:13 2020 -0500

    Address suggestion by @tsalo

commit 45210a9
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:32:20 2020 -0500

    Wording

commit 66ba5a5
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:31:40 2020 -0500

    RECOMMENDED --> MUST for adding an application def to the appdx

commit 5611fac
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:29:21 2020 -0500

    Improve the appendix

commit 6d3bbea
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 2 16:12:04 2020 -0500

    Address suggestions by @tsalo

commit bcb0223
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:37:26 2020 -0400

    [ADD] Link to the appendix

commit 44e760f
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:28:38 2020 -0400

    [ADD] Appendix - File collections

    - For parametrically linked file collections

commit 523b1c1
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:27:52 2020 -0400

    [ADD] Parametrically linked file collections

    - Description
@effigies
ENH: Link to all BEP-001 entities
a736bb4
@effigies
STY: Escape asterisk, adjust table widths
159df77
@effigies effigies mentioned this pull request Dec 1, 2020
Closed
@agahkarakuzu
Copy link
Contributor

Thank you @effigies I will address the comments by @sappelhoff here, whenever it is ready. I can wait till you make all the checks pass.

@effigies
Copy link
Collaborator Author

effigies commented Dec 1, 2020

The current linkcheck failure looks stochastic with Zenodo having a 500 error. Visiting the link manually resolves fine. I would go ahead now.

@agahkarakuzu
Copy link
Contributor

@sappelhoff in 46edf44 I moved the \* text to the qMRI Appendix. I will edit that Appendix and make a PR for that after this is closed.

Until then, Please see qMRI appendix in the table can remain as plain text rather than a broken hyperlink if that's OK with you.

effigies
effigies commented Dec 1, 2020
View reviewed changes
Copy link
Collaborator Author

@effigies effigies left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks good to me (I can't approve, as the submitter).

I made a number of suggestions that are mostly reworking the line spacing so that sentences are a bit more readable in source form, but should have no impact on the output.

I've also marked where I've made some semantic suggestions. Feel free to reject if I've gotten them wrong.

src/02-common-principles.md Outdated Show resolved Hide resolved
src/02-common-principles.md Outdated Show resolved Hide resolved
src/02-common-principles.md Outdated Show resolved Hide resolved
src/02-common-principles.md Outdated Show resolved Hide resolved
src/02-common-principles.md Outdated Show resolved Hide resolved
src/99-appendices/10-file-collections.md Outdated Show resolved Hide resolved
sappelhoff
sappelhoff approved these changes Dec 1, 2020
View reviewed changes
Copy link
Member

@sappelhoff sappelhoff left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks, LGTM once Chris' suggestions are worked in.

agahkarakuzu and others added 6 commits December 1, 2020 14:04
@agahkarakuzu @effigies
Update src/02-common-principles.md
e86eb57 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu @effigies
Update src/02-common-principles.md
b8edf74 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu @effigies
Update src/02-common-principles.md
daced12 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu @effigies
Update src/99-appendices/10-file-collections.md
6943c83 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu @effigies
Update src/02-common-principles.md
7372213 
Thank you @effigies!

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu @effigies
Update src/02-common-principles.md
4949642 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu
Copy link
Contributor

agahkarakuzu commented Dec 1, 2020 •
edited
Loading

Thank you so much @effigies for your thorough review and suggestions!

@effigies effigies merged commit 614b811 into bids-standard:master Dec 1, 2020
@effigies effigies deleted the file-collections-redux branch December 1, 2020 19:50
sappelhoff added a commit that referenced this pull request Dec 2, 2020
@sappelhoff @bids-maintenance
@agahkarakuzu @effigies
update bep005 with latest master + resolve conflict (#689)
ef6f851 
* [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 <stefan.appelhoff@mailbox.org>

* Update src/schema/entities.yaml

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* table fix by @sappelhoff

* Conditional requirement

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* [ENH] BEP001 - Entity-linked file collections (#688)

* Squashed commit of the following:

commit 8e1ac5f
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 11:09:24 2020 +0100

    fix links and latin

commit 27c9b41
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 10:03:51 2020 +0100

    remove latin

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 7d87070
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:46:47 2020 -0500

    Update src/99-appendices/10-file-collections.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit b137a9e
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:45:19 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit d7897b8
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:40 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 09e9d32
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:15 2020 -0500

    Commit suggestion

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 009a9ab
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:43:00 2020 -0500

    Add file-collecitons appendix to the TOC

commit 8f6c4df
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:41:13 2020 -0500

    Address suggestion by @tsalo

commit 45210a9
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:32:20 2020 -0500

    Wording

commit 66ba5a5
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:31:40 2020 -0500

    RECOMMENDED --> MUST for adding an application def to the appdx

commit 5611fac
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:29:21 2020 -0500

    Improve the appendix

commit 6d3bbea
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 2 16:12:04 2020 -0500

    Address suggestions by @tsalo

commit bcb0223
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:37:26 2020 -0400

    [ADD] Link to the appendix

commit 44e760f
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:28:38 2020 -0400

    [ADD] Appendix - File collections

    - For parametrically linked file collections

commit 523b1c1
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
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 <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/10-file-collections.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Thank you @effigies!

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: Agah Karakuzu <agahkarakuzu@gmail.com>

* [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 <effigies@gmail.com>

* 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 <effigies@gmail.com>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update config.yml

* Update readthedocs.yml

Co-authored-by: bids-maintenance <bids.maintenance@gmail.com>
Co-authored-by: Agah <agahkarakuzu@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
This was referenced Dec 9, 2020
Closed
Closed
sappelhoff added a commit that referenced this pull request Jan 15, 2021
@sappelhoff @HenkMutsaerts
@patsycle @effigies @guiomar @Remi-Gau @bids-maintenance @agahkarakuzu @tsalo
[ENH] Bep 005: Arterial Spin Labeling (#669)
d794736 
* [ENH] Bep 005: Arterial Spin Labeling (#652)



Co-authored-by: Patricia Clement <41481345+patsycle@users.noreply.github.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* 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 <stefan.appelhoff@mailbox.org>

* Update src/schema/entities.yaml

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* table fix by @sappelhoff

* Conditional requirement

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* [ENH] BEP001 - Entity-linked file collections (#688)

* Squashed commit of the following:

commit 8e1ac5f
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 11:09:24 2020 +0100

    fix links and latin

commit 27c9b41
Author: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date:   Fri Nov 27 10:03:51 2020 +0100

    remove latin

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 7d87070
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:46:47 2020 -0500

    Update src/99-appendices/10-file-collections.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit b137a9e
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:45:19 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit d7897b8
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:40 2020 -0500

    Update src/02-common-principles.md

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 09e9d32
Author: Agah <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:44:15 2020 -0500

    Commit suggestion

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>

commit 009a9ab
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:43:00 2020 -0500

    Add file-collecitons appendix to the TOC

commit 8f6c4df
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 23 08:41:13 2020 -0500

    Address suggestion by @tsalo

commit 45210a9
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:32:20 2020 -0500

    Wording

commit 66ba5a5
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:31:40 2020 -0500

    RECOMMENDED --> MUST for adding an application def to the appdx

commit 5611fac
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Wed Nov 11 14:29:21 2020 -0500

    Improve the appendix

commit 6d3bbea
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Mon Nov 2 16:12:04 2020 -0500

    Address suggestions by @tsalo

commit bcb0223
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:37:26 2020 -0400

    [ADD] Link to the appendix

commit 44e760f
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
Date:   Tue Oct 27 21:28:38 2020 -0400

    [ADD] Appendix - File collections

    - For parametrically linked file collections

commit 523b1c1
Author: Agah Karakuzu <agahkarakuzu@gmail.com>
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 <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/10-file-collections.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Thank you @effigies!

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/02-common-principles.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: Agah Karakuzu <agahkarakuzu@gmail.com>

* [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 <effigies@gmail.com>

* 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 <effigies@gmail.com>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update config.yml

* Update readthedocs.yml

Co-authored-by: bids-maintenance <bids.maintenance@gmail.com>
Co-authored-by: Agah <agahkarakuzu@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* 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 <markiewicz@stanford.edu>

* update description aslcontext

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* update PCASLType and CASLType

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>

* 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 <markiewicz@stanford.edu>

* 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 <henkjanmutsaerts@gmail.com>
Co-authored-by: Patricia Clement <41481345+patsycle@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: bids-maintenance <bids.maintenance@gmail.com>
Co-authored-by: Agah <agahkarakuzu@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sappelhoff sappelhoff sappelhoff approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@effigies @agahkarakuzu @sappelhoff