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November 29, 2017 12:54PM
The zeitgeist for AFNI's data layout and the zeitgeist for BIDS' data layout aren't well-matched. AFNI wants everything for the subject in one directory and BIDS wants each type of data in a separate directory. For example, for one subject, I currently have at least 6 relevant directories with the data:

sub-127608/ses-Session1/anat
sub-127608/ses-Session1/fmap
sub-127608/ses-Session1/func
derivatives/fmriprep/sub-127608/ses-Session1/anat
derivatives/fmriprep/sub-127608/ses-Session1/func
derivatives/bold/sub-127608/ses-Session1

My solution at the moment is to define a bash function (or use a shell-script) that uses find to help:
bsafni() {
  afni -DAFNI_SESSTRAIL=4 `find . -type d \( -wholename "*${1}*func" -o -wholename "*${1}*anat" -o -wholename "*${1}*fmap" -o -wholename "*derivatives/bold/*${1}*" \) | tr '\n' ' '`
}

so I can bsafni 127608 and then switch the session to "all datasets" (huge plus that feature!).

Are there other solutions people have out there to working with these two together?

Craig
Subject Author Posted

AFNI and BIDS

celstark November 29, 2017 12:54PM

Re: AFNI and BIDS

Bob Cox November 30, 2017 11:14AM

Re: AFNI and BIDS

celstark November 30, 2017 05:15PM

Re: AFNI and BIDS

daisyburr January 30, 2018 12:19PM

Re: AFNI and BIDS

Bob Cox February 01, 2018 04:01PM

Re: AFNI and BIDS

Bob Cox February 02, 2018 03:28PM

Re: AFNI and BIDS

RWCox February 03, 2018 08:47AM

Re: AFNI and BIDS

celstark February 23, 2018 03:58PM

Re: AFNI and BIDS

RWCox February 25, 2018 10:59AM

Re: AFNI and BIDS

dowdlelt March 28, 2018 10:30AM

Re: AFNI and BIDS

Dillon Plunkett April 05, 2021 12:52PM



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