BIDS Brain atlases extension

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Oscar Esteban

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May 28, 2018, 2:46:52 PM5/28/18
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Hi there,

I want to propose a very limited use-case, but IMHO it would improve writing workflows very much. Currently, there are plenty of different templates (all ICBM152 flavors, Collins27, OASIS, NKI, freesurfer's, etc.) and all have varying names to the images included within.

Without thinking too much, I would suggest something along the lines of:

templates_dir/
    tpl-ICBM152NLin2009cAsym/
        template_description.json
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01.json
        tpl-ICBM152NLin2009cAsym_space-MNI_res-02.json
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_brainmask.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_class-CSF_probtissue.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_class-GM_probtissue.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_class-WM_probtissue.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-01_T2w.nii.gz
        tpl-ICBM152NLin2009cAsym_space-MNI_res-02_BOLD.nii.gz


template_description.json would contain info about the template:

{
  "name": "ICBM 152 Nonlinear Asymmetric v. 2009c atlas",
  "version": "2009c",
  "id": "ICBM152NLin2009cAsym",
  "authors": [ ... ],
  "citation": [ ... ]
}

Then, conventional json sidecars would work. E.g. tpl-ICBM152NLin2009cAsym_space-MNI_res-01.json:

{
  "resolution": [1, 1, 1],
  "units": "mm"
}


Please note that 01 is an index, and thus tpl-ICBM152NLin2009cAsym_space-MNI_res-02.json could be:
{
  "resolution": [1, 1, 4],
  "units": "mm"
}

AFAIK, this doesn't exist yet in BIDS. WDYT?

Cheers,
Oscar

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Oscar Esteban, Ph.D.
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Stanford University

Satrajit Ghosh

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May 28, 2018, 3:10:09 PM5/28/18
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hi oscar,

i'm sure JB will pitch in. this is what the INCF HAWG group was trying to do. we had a lot of discussions on this already and it would be useful to consider that as a starting point.

See the PR #17

mike halle implemented a version of this for his medical atlas viewer. here is a brain example:

cheers,

satra

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Chris Gorgolewski

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May 28, 2018, 3:16:42 PM5/28/18
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Hi,

@oscar In general this already been covered in BIDS Derivatives https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit#heading=h.irsejzqb17h1. But perhaps you intended something else? A structured file repository of commonly used templates? Something that would be independent of any particular dataset? I can see such repository (with harmonized description of all templates) to be quite useful.

@satra I think Oscar meant "templates" (coregistration targets) not atlases (definitions of ROIs).

Best,
Chris


cheers,

satra

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Oscar Esteban

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May 29, 2018, 2:22:49 PM5/29/18
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Hi,

Yes, as Chris was suggesting, I think that having a consistent interface to various templates (that, as Satra said, would also probably come with the corresponding atlas information) would be the goal. Once that is defined, it would be fairly simple to create the repository structured in that way. 

I definitely agree on reusing as much as we can from the BIDS Derivatives extension. E.g. the template labels, for sure. And I don't mind at all that this becomes part of that extension too (i.e. as a particular use-case)! If you think this is worth a shot, please let me know and I'll start outlying it on the draft.

Cheers,
Oscar


cheers,

satra

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Chris Gorgolewski

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May 29, 2018, 2:30:29 PM5/29/18
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I feel that if the goal is a centralized repository of easy to access templates with harmonized metadata there might not be a need for a long process of finding a community consensus for a standard. After all new templates are created very rarely, so just taking existing templates (for example those listed in the BIDS derivatives document) and putting all of them in a github repo with neat naming convention and harmonized metadata would be very helpful for a lot of people.

Best,
Chris


cheers,

satra

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Oscar Esteban, Ph.D.
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Stanford University

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Henk-Jan Mutsaerts

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May 29, 2018, 3:03:45 PM5/29/18
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Yes I +1 that. Also, it would be great to have a document that reviews the differences between the main atlases, and quantifies them, either in an original paper or consensus review.


Best wishes/hartelijke groet,

 

 

Henk(-Jan) Mutsaerts, MD PhD

VUmc Amsterdam/AMC Amsterdam/UMCU Utrecht
UMCG Groningen/Sunnybrook Toronto/RIT NY

Phone: +31 6 4390 8284; Skype: hj.mutsaerts



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Guillaume Flandin

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May 30, 2018, 6:18:40 AM5/30/18
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Hi,

This is something Jason Bohland looked at about a decade ago. The outcome was OBART (Online Brain Atlas Reconciliation Tool):
  http://qnl.bu.edu/obart
Having been involved in the Human Atlasing Working Group mentioned by Satra above, I would advocate for a community standard for encoding atlas metadata but, yes, it takes time and energy...

Best,
Guillaume.


cheers,

satra

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Vince Calhoun

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May 30, 2018, 6:33:33 AM5/30/18
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Agreed this is useful.  Would be nice to do this in a way that was invariant to the spatial resolution of the sampled space as well.   Ideally in a way that can also include ‘fuzzy’ atlases (like spatial ICA maps).  ;-)

 

Best,

 

VDC

 

cheers,

satra

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Oscar Esteban, Ph.D.
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Henk-Jan Mutsaerts

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May 30, 2018, 6:41:39 AM5/30/18
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Dear Guillaume,


Thanks for pointing this out! I have actually created a very similar tool for comparing clusters from voxel-based analyses to atlas regions, for our ASL standardized pipeline (ExploreASL). I will certainly make sure to refer to this work.

Best, Henk

Best wishes/hartelijke groet,

 

 

Henk(-Jan) Mutsaerts, MD PhD

VUmc Amsterdam/AMC Amsterdam/UMCU Utrecht
UMCG Groningen/Sunnybrook Toronto/RIT NY

Phone: +31 6 4390 8284; Skype: hj.mutsaerts


cheers,

satra

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Oscar Esteban

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May 30, 2018, 11:44:35 AM5/30/18
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Dear all,

Thanks a lot for all the resources about atlases, I will definitely check them out.

However, my intent here was a bit more humble. Basically, providing a standardize way of selecting a template from within a pool of them (a repository as Chris mentioned, when I go ahead and share it conveniently). Atlases would be there for convenience and fast application, but I was not intending to enter the realm of organizing them (Satra and Guillaume gave pointers to efforts in that direction).

My first take at this has resulted in the following structure:

tpl-MNI152NLin2009cAsym
├── CHANGES
├── template_description.json
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_brainmask.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-CSF_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-GM_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_class-WM_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-carpet_atlas.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-eyemask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-facemask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-headmask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_PD.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w_brain.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T1w.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-01_T2w.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-CSF_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-GM_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_class-WM_probtissue.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-carpet_atlas.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-eyemask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-facemask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_label-headmask_roi.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_PD.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T1w_brain.nii.gz
├── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T1w.nii.gz
└── tpl-MNI152NLin2009cAsym_space-MNI_res-02_T2w.nii.gz
tpl-OASIS30ANTs
├── CHANGES
├── template_description.json
├── tpl-OASIS30ANTs_res-01_brainmask.nii.gz
├── tpl-OASIS30ANTs_res-01_class-brainmask_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-bstem_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-Cerebellum_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-CGM_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-CSF_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-DGM_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_class-WM_probtissue.nii.gz
├── tpl-OASIS30ANTs_res-01_label-BrainCerebellumExtraction_roi.nii.gz
├── tpl-OASIS30ANTs_res-01_label-BrainCerebellumRegistration_roi.nii.gz
├── tpl-OASIS30ANTs_res-01_T1w_brain.nii.gz
├── tpl-OASIS30ANTs_res-01_T1w.nii.gz
├── tpl-OASIS30ANTs_res-01_variant-4_dtissue.nii.gz
└── tpl-OASIS30ANTs_res-01_variant-6_dtissue.nii.gz
As you can see, the templates are not required to have specific instances or define atlases (i.e. I did not include any atlas for the OASIS30ANTs).

Cheers,
Oscar


cheers,

satra

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