Closed dkp closed 5 years ago
yarikoptic
commented
5 years ago Reproin convention is largely just bids. So it is _key-value pairs, but starts with the datatype (anat/functions) and optional suffix/modality (T1w). With all things underscores, would not be buddy, and harder to parse visually and programmatically. If they is not enough of the story, reopen ;-)
dkp
commented
5 years ago Hi Yaroslav,
That helps. Maybe you could provide just a little more clarification. I see that reproin is largely BIDS and I think I understand the use of dashes for key-value pairs as contrasted with the underscore in BIDS. So, for the reproin scheme, we begin with seqtype (e.g., anat, func, fmap or dwi). After seqtype we can have a label; seqtype and label are joined by a dash. So we get anat-scout and anat-T1W etc.
Given line 47 in https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py, I would expect the func seqtype to follow the same pattern, like so: func-bold
However, the func seqtype is not followed by the label bold in any examples I see:
1) https://docs.google.com/document/d/1EivqiAnbTGPRjav3eOsmqbOMJR5phdLrto5gFNBFpdE/edit#heading=h.t15gvk28p66k 2) Figure 1 on the github site: https://github.com/repronim/reproin 3) https://github.com/ReproNim/reproin/blob/master/docs/walkthrough-1.md
After a little experimentation, I see that func-bold_task-rest in the protocol name produces the same NIFTI file names as func_task-rest. I'm guessing bold is the default case for func data, and so not necessary to specify? Or is something else going on?
Thanks for your patience,
-Dianne
On Mon, Feb 11, 2019 at 5:45 PM Yaroslav Halchenko notifications@github.com wrote:
Reproin convention is largely just bids. So it is _key-value pairs, but starts with the datatype (anat/functions) and optional suffix/modality (T1w). With all things underscores, would not be buddy, and harder to parse visually and programmatically. If they is not enough of the story, reopen ;-)
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yarikoptic
commented
5 years ago re no "bold" - check out https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L47 so yes - "bold" is the default for "func", and "T1w" is the default for anat"
dkp
commented
5 years ago okay, I get it. Thanks, -D
On Mon, Feb 11, 2019 at 9:41 PM Yaroslav Halchenko notifications@github.com wrote:
re no "bold" - check out https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L47 so yes - "bold" is the default for "func", and "T1w" is the default for anat"
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-- Dianne Patterson, Ph.D. Research Scientist dkp@email.arizona.edu dkp@u.arizona.edu or diannepat@gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill)
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Antipiphany: That moment when you realize how little you actually know
I'm going to talk about reproin on Friday, and I am going to be asked why the reproin naming scheme is different for anat than for anything else. Why would anat-T1W_acq-MPRAGE be right instead of anat_T1W_acq_MPRAGE? It seems inconsistent with the other modalities, so there must be a story.
Thanks