Enforcing TE order for multi-echo fMRI

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Elizabeth DuPre

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Mar 1, 2018, 6:52:57 PM3/1/18
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Hi all,

This is a detail in the current BIDS spec for multi-echo fMRI which does not seem to be settled. It would be great to enforce an ordering for the multiple TEs in multi-echo fMRI data. Currently, it seems that any sequential ordering is accepted, with `*_echo-1*` as either the longest or the shortest echo.

Is there any objection to standardizing this so that `*_echo-1*` is always the shortest echo (i.e., has the shortest TE), and all subsequent echos occur in sequential order ? Would love to know your thoughts !

Thanks,

Elizabeth

Chris Gorgolewski

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Mar 2, 2018, 8:41:48 AM3/2/18
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Thanks for bringing this up. +1 for adding this clarification to the spec.

Best,
Chris

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Daniel Handwerker

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Mar 2, 2018, 9:00:50 AM3/2/18
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As another multi-echo user, I have no objections. Perhaps there's a big-endian subgroup of multi-echo users somewhere who put the longest echo first, but every data set I've seen puts the shortest echo first. This might be useful to standardize before such variation arises.

Best,

Dan

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Harms, Michael

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Mar 2, 2018, 9:13:03 AM3/2/18
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While that could be *suggested* for BIDS 1.x, wouldn’t *requiring* that under the 1.x spec represent a “backwards incompatibility”, since there may possibly be datasets where such ordering isn’t the case?

 

Also, this is a broader issue than just multi-echo, and could be applied to any key/tag with an <index> component.  E.g., Should there be any expectation that the <index> value in “run-<index>” is sequentially incremented according to the temporal order of acquisition?

 

Cheers,

-MH

 

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Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

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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, March 2, 2018 at 7:42 AM
To: bids-discussion <bids-di...@googlegroups.com>
Subject: Re: [bids-discussion] Enforcing TE order for multi-echo fMRI

 

Thanks for bringing this up. +1 for adding this clarification to the spec.

Best,
Chris

On Mar 1, 2018 3:52 PM, "Elizabeth DuPre" <elizabet...@gmail.com> wrote:

Hi all,

This is a detail in the current BIDS spec for multi-echo fMRI which does not seem to be settled. It would be great to enforce an ordering for the multiple TEs in multi-echo fMRI data. Currently, it seems that any sequential ordering is accepted, with `*_echo-1*` as either the longest or the shortest echo.

Is there any objection to standardizing this so that `*_echo-1*` is always the shortest echo (i.e., has the shortest TE), and all subsequent echos occur in sequential order ? Would love to know your thoughts !

Thanks,

Elizabeth

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Chris Gorgolewski

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Mar 3, 2018, 12:59:09 PM3/3/18
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That's a good point about backward compatibility.

As for runs - this could potentially also apply, but with the same compatibility constraints you brought up.

Best,
Chris

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Elizabeth DuPre

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Mar 3, 2018, 1:21:59 PM3/3/18
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 Thanks so much for the feedback !

Regarding the issue of runs, I'm not sure that I directly see the connection. Echos have a different relationship to one another than runs do, as echos are usually not considered independently. The example I can immediately think of where run ordering matters is pre/post intervention, but in the BIDS examples I've seen, this is usually specified in another key/value pair. Could you please clarify why the sequential concern would apply to all key values with a numerical index ?

Thanks again,

Elizabeth

Chris Gorgolewski

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Mar 3, 2018, 4:57:07 PM3/3/18
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Hi,

The connection between run and echo filename keys is not direct. They both enforce indices as values, they both relate to time (but in slightly different way). The way I understood Michael's comment was that if we are thinking about specifying that "echo-2" has to have large TE value than "echo-1" we might also want to specify that "run-2" has to be acquired after "run-1". Those two additional clarifications are not however linked to each other and decisions about them could be done independently.

They do, however, share the same backward compatibility concern. If there is a dataset out there that used reverse order of echo when saving files (because that was not specified) and a new version of spec will require a particular order that dataset will not be compatible with it.

I hope this clarified things a little.

Best,
Chris

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Elizabeth DuPre

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Mar 4, 2018, 11:08:47 AM3/4/18
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Thanks for clarifying, Chris ! Yes, I think my confusion was if these decisions were linked. I do appreciate the backwards compatibility concern, so if there are no other concerns-- specifically with the idea of enforcing echo ordering-- I can add it as a suggestion to the BIDS 2.0 document.

Best,

Elizabeth

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Chris Gorgolewski

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Mar 4, 2018, 11:21:36 AM3/4/18
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Great. Thanks!

Best,
Chris

On Mar 4, 2018 8:08 AM, "Elizabeth DuPre" <elizabet...@gmail.com> wrote:
Thanks for clarifying, Chris ! Yes, I think my confusion was if these decisions were linked. I do appreciate the backwards compatibility concern, so if there are no other concerns-- specifically with the idea of enforcing echo ordering-- I can add it as a suggestion to the BIDS 2.0 document.

Best,

Elizabeth
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