Add Siemens 2D MB PCASL example

[aptinis]

No description provided.

[aptinis]

Hi there, this is the example BIDS dataset with the Siemens 2D MB Multi-delay PCASL (the same sequence used by HCP Aging) to support the PR [ENH] Add noRF and n/a ASL volume types addressing aslcontext.tsv dummy volumes. I am looking for feedback and have a couple of questions/comments.

1. Are there any conventions to follow for naming the dataset?

2. When I ran python tools/print_dataset_listing.py it unexpectedly modified ds001 in the dataset_listing.tsv and README.md by (incorrectly?) adding CITATION to the suffixes. In order to prevent this behaviour I added CITATION to the list of suffixes to remove. Let me know if this is okay.

3. BIDS validation is currently failing.

There are 2 issues:

• the BIDS validation will fail with error: TSV_VALUE_INCORRECT_TYPE (volume_type) due to the inclusion of noRF in the ASL context file (the purpose of this example is to update the BIDS spec to include this new volume type). Will this require a .SKIP_VALIDATION or .bidsignore file due to lack of coverage in the bids-validator?

• I believe there is a bug with the BIDS validator (Schema version 0.11.0) error: JSON_SCHEMA_VALIDATION_ERROR (PostLabelingDelay) which expects PostLabelingDelay to be a number although according to the BIDS spec it can also be an array of numbers.

4. For the noRF volumes I've set the PostLabelingDelay and LabelingDuration to 0. I have left the RepetitionTimePreparation to be the same as the tag/control volumes (although I'm not 100% sure if that's accurate).

Please let me know I've missed anything (I am new to contributing to open source projects!) or have any feedback. Thank you!

[effigies]

 	[ERROR] JSON_SCHEMA_VALIDATION_ERROR Invalid JSON sidecar file. The sidecar is not formatted according the schema.
		PostLabelingDelay
		/sub-1/perf/sub-1_asl.json - must be number
		/sub-1/perf/sub-1_asl.json - must be > 0

The issue here is that we have an exclusive minimum:

PostLabelingDelay:
  name: PostLabelingDelay
  display_name: Post Labeling Delay
  description: |
    This is the postlabeling delay (PLD) time, in seconds, after the end of the
    labeling (for `"CASL"` or `"PCASL"`) or middle of the labeling pulse
    (for `"PASL"`) until the middle of the excitation pulse applied to the
    imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
    Can be a number (for a single-PLD time series) or an array of numbers
    (for multi-PLD and Look-Locker).
    In the latter case, the array of numbers contains the PLD of each volume,
    namely each `control` and `label`, in the acquisition order.
    Any image within the time-series without a PLD, for example an `m0scan`,
    is indicated by a zero.
    Based on DICOM Tags 0018, 9079 `Inversion Times` and 0018, 0082
    `InversionTime`.
  anyOf:
    - type: number
      exclusiveMinimum: 0
      unit: s
    - type: array
      items:
        type: number
        exclusiveMinimum: 0
        unit: s

I pushed to @tsalo's branch, so will rerun these now.

[effigies]

Pending the upstream PR

[Remi-Gau]

Thanks for catching that one

[Remi-Gau]

unrelated to this PR but this little 'trick' to test a version of the schema related to a PR in the spec should be mentioned in our doc, so that BEP leads know how to start testing their datasets

[Remi-Gau]

#1864 was merged so this PR should be updated

[Remi-Gau]

good with me