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Pediatric template #24

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oesteban opened this Issue Apr 30, 2018 · 7 comments

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@oesteban
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commented Apr 30, 2018

From poldracklab/fmriprep#817 (comment).

It would be handy having a pediatric template as proposed in that comment (https://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases). This would probably deprecate (partially) #330.

@taehol, would you be interested in trying to implement this one (and becoming one of FMRIPREP's contributors)? We can walk you through the process.

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commented May 1, 2018

That sounds interesting! In fact, I am not an extensive python user but bash, so not sure how much I can contribute for fMRI-PREP.

Anyway, to share what I am now working on, the pipeline I am now scripting (sorry I am not using FMRIPREP now) for baby resting data is using IBIS templates (http://www.bic.mni.mcgill.ca/autism/) for registration and IDEA's aal atlas (https://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases) for extracting time-series based on ANTs. Either works fine now. I have also tweaked ICA-AROMA script to use ANTs matrix and my own templates (in this case, I use IBIS-T1-1yr-2mm-brain template; the original template is on 1-mm space but I converted it to 2 mm simply because my baby epi is 2 mm and do not want to do up-sampling it), and so far so good for registration and reasonable the edge and csf fraction detection (however ICA-AROMA needs to be tested repeatedly).

non-linear spatial normalization (individual T1 -> IBIS-T1-1yrs)
qc ants_highres2standard

IDEA's 1-yrs-aal-parcellation-atlas -> individual T1 space
struct

Please let me know if there is something that I can be helpful to improve FMRIPREP pipeline.

@ihashi3

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commented Oct 16, 2018

I'm interested in using a paediatric atlas (http://nist.mni.mcgill.ca/?p=974) for registration in FMRIPREP, was wondering how I could add this into the script instead of using an adult atlas.

Thank you!

@oesteban

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commented Oct 16, 2018

Hi all, I'm preparing a PR to standardize the use of templates and will update the wiki with a step-by-step guide to adding new templates. Will report back asap. Thanks a lot for the interest!

cc/ @rciric for the rodent template

@ihashi3

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commented Oct 16, 2018

Thank you very much!

@switt4

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commented Oct 18, 2018

Hi,

I am trying to help get a few studies up and running with fmriprep using other templates (pediatric/neonate and macaque).

Sorry for the perhaps somewhat obvious question, but which wiki will be updated with the guide to adding new templates, the one associated with this github or the main fmriprep documentation page?

Thanks,

suzanne

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commented Oct 19, 2018

Hi Suzanne, I'm still working that out. Will update when ready.

@switt4

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commented Nov 16, 2018

Hi,

Are there any more updates as to when the guide for how to change templates is going to be released? I cannot seem to find any more information on either the fMRIprep documentation site or the github wiki.

Thanks again,

suzanne

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