ASL - CBF map

[Reza Eghbali]

What should I do with CBF map? Reading the ASL instructions, it seems like BIDS only supports a complete ASL time series stored as a 4D NIfTI. In my case, I have the CBF map generated by the MRI machine as a 3D NIfTI.

[tibor...@gmail.com]

Hi Reza,

 

This case seems similar to the scanner-generated DWI estimates (ADC, FA, trace, etc.). Since the CBF map is derived from the raw data, similar to how the DWI estimates are derived from the raw DWI data, I suggest including and reporting it as ASL-derivative, including the vendor, model, and software version of your scanner.

 

Please, see the BIDS specification for further guidance on how to store a derived dataset (Common principles) and report a pipeline (Modality agnostic files).

 

Kind regards,

Tibor

 

Tibor Auer, MD, PhD, FHEA

Lecturer in Biological Psychology

School of Psychology, Faculty of Health and Medical Sciences

University of Surrey, Guildford GU2 7XH

T.A...@surrey.ac.uk

@TiborAuer

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[Dr Cyril, Pernet]

Hi all,

this is not gonna help Reza, sorry ... but

- for single volume images, the common view is whatever comes out of the scanner is raw, for instance T1w with gradient non linearity correction is raw, yet this is a post-hoc correction, same thing with the UNIT image from MP2RAGE, even the phasediff image in fieldmap is computed post-hoc and it is stored as raw.

- anything that comes from time series tend to be seen as derivative, as Tibor pointed out, FA, ADC, MD for DWI and CBF for ASF

We could keep that distinction single volume vs time series, but it doesn't seem based on any computational principle -- or we need to decide as a community and resolve this either all derivatives (but it would break lots of backward stuff) or we accept 'anything out of the scanner'  as raw, implying you could have FA,ADC,MD,CBF in raw (out of the scanner) and FA,ADC,MD,CBF in derivatives (out of a given analysis pipeline) that would be distinguishable only from the position in the tree and json files (or impose an extra key-value in the name in the later case).

Cyril

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[Earl, Eric (NIH/NIMH) [C]]

Reza,

 

I re-read the section on ASL in the specification:

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#arterial-spin-labeling-perfusion-data

 

As I understand it on my read, ASL is one 4D NIfTI, but it’s just 4D because it’s a result of concatenating the 3D images yourself and providing and “aslcontext.tsv” that says what volume is what in the 4D NIfTI. I hope that helps.

 

Warm regards,

 

Eric Earl [C]

Scientist

 

eric...@nih.gov

(503) 752-8549

 

NIMH IRP Data Science & Sharing Team

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[Henk-Jan Mutsaerts (Henk)]

Sorry to only read this now. Principally this is indeed a derivative but if your scanner doesn’t export the raw images (eg GE, because they do a complex subtraction on the scanner) then you should consider these raw. You can specify this in the aslcontext.tsv

Best, Henk

On 12 Jun 2023, at 17:52, 'Earl, Eric (NIH/NIMH) [C]' via bids-discussion <bids-di...@googlegroups.com> wrote:



Reza,

 

I re-read the section on ASL in the specification:

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#arterial-spin-labeling-perfusion-data

 

As I understand it on my read, ASL is one 4D NIfTI, but it’s just 4D because it’s a result of concatenating the 3D images yourself and providing and “aslcontext.tsv” that says what volume is what in the 4D NIfTI. I hope that helps.

 

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