Re: [bids-discussion] [BEP001] rec- (not acq-) vs part- keys

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Kirstie Whitaker

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Jul 19, 2018, 3:41:44 AM7/19/18

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Hi everyone,

Note that I've updated the subject line - I'd meant to write rec- vs part- and the acq- was just a typo on my part! I don't think it's derailed the discussion too much, I think everyone's been discussing rec- vs part- anyway, but I just wanted to apologise for the mistake and make sure that we're all on the same page!

So, rec- vs part-:

Michael, at almost exactly the same time as you were writing your email, there were a few of us on a call discussing various questions relating to the BEP001 proposal. The notes are at: https://docs.google.com/document/d/17Ecs-3_2MxLt-D7bdLNrpYFJMHEQMjN6EUuM1ogujvw/

We discussed this point and acknowledged the point you raised but ultimately voted to incorporate part-.....with a caveat to check with you first!

There's two arguments that we followed: 1) that these are two projections of the same information, so the part- tag would be very well constrained, while the different types of reconstructions are likely to grow over time, and 2) that most of us felt that mag & phase were intuitively different parts of the same information, rather than reconstructions of that information.

So now, the question is......how strongly do you feel about the concern of adding more tags? The goal of the hangout was to move BEP 001 forwards, so a decision is the most important outcome!

I'm super happy to follow up with you on a call or off list if that's helpful?

On 18 July 2018 at 16:11, Harms, Michael <mha...@wustl.edu> wrote:

But they *could* in principle be recons on the scanner. My 2c is that a proliferation of tags specific to each MR modality is not conducive to harmony across the specification as a whole.

Cheers,

-MH

--

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO 63110                          Email: mha...@wustl.edu

From: <bids-discussion@googlegroups.com> on behalf of Pamela LaMontagne <ppers...@gmail.com>
Reply-To: "bids-discussion@googlegroups.com" <bids-discussion@googlegroups.com>
Date: Wednesday, July 18, 2018 at 10:08 AM
To: bids-discussion <bids-discussion@googlegroups.com>

Subject: Re: [bids-discussion] [BEP001] acq- vs part- keys

For SWI the mag and phase are different parts of input to the SWI image which can be reconstructed on the scanner or in separate software. They are not actually reconstructions in this case

On Tuesday, July 17, 2018 at 10:33:11 AM UTC-5, Harms, Michael wrote:

Hi,

What exactly is “part” intended to convey? To me, “phase” and “mag” are different types of recons, and thus most naturally related to the “rec” tag.

Cheers,

-MH

--

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

St. Louis, MO 63110                          Email: mha...@wustl.edu

From: <bids-di...@googlegroups.com> on behalf of Chris Gorgolewski <krzysztof....@gmail.com>
Reply-To: "bids-di...@googlegroups.com" <bids-di...@googlegroups.com>
Date: Friday, July 13, 2018 at 10:07 PM
To: bids-discussion <bids-di...@googlegroups.com>
Subject: Re: [bids-discussion] [BEP001] acq- vs part- keys

One thing to consider here is that values of rec are currently free form and proposed part would be controlled vocabulary with two possible values "phase" and "mag". Thus I think in this case part makes more sense.

Best,

Chris

On Fri, Jul 13, 2018 at 9:32 AM Kirstie Whitaker <kw...@cam.ac.uk> wrote:

Hi BIDS community & BEP 001 devs,

There's a question that Michael Harms has added as a comment to the BEP001 proposal that I'd like to move forwards a decision on.

Here's a link to the comment but I've copied and pasted it here:

> Is the _part tag new to this extension? (I didn't find mention of it in the main spec). What does "part" stand for? Couldn't this be handled via the already existing _rec tag (e.g, _rec-magn and _rec-phase)?

Here's the template, copied from the BEP001 extension (link):

Template:

sub-<participant_label>/[ses-<session_label>/]

anat/

sub-<participant_label>[_ses-<session_label>][_acq-<label>][_rec-<label>][_fa-<index>][_inv-<index>][_echo-<index>][_part-<phase|mag>][_run-<index>]_<sequence_label>.nii[.gz]

Here's the description of the part- tag from the BEP001 proposal (link):

> The optional key [_part-<phase|mag>] allows for storing phase and magnitude images. In its absence the image is assumed to be magnitude.

And here's the decription of the rec- tag from the BIDS specification (link):

> Similarly the OPTIONAL “rec-<label>” key/value can be used to distinguish different reconstruction algorithms (for example ones using motion correction)

Any thoughts on whether we need part- or whether rec- would suffice?

It looks like we definitely would need to update the definition of rec- in the main BIDS spec to be a little clearer about what it means, but I don't have strong feelings either way!

Kx

--

Kirstie Whitaker, PhD

Research Fellow, Alan Turing Institute

Research Associate, University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: https://whitakerlab.github.io

Twitter: @kirstie_j

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We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
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We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
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Kirstie Whitaker, PhD

Research Fellow, Alan Turing Institute

Research Associate, University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: https://whitakerlab.github.io

Twitter: @kirstie_j

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