Susceptibility distortion correction not performed in fMRIPrep

[erbenne]

My preprocessing summary reports all say: Susceptibility distortion correction: None
but I have fieldmap scans–and I don’t see a configuration setting for fieldmap sdc
Grateful for any help!!

[Steven]

Hello,

Do your fieldmap JSON files have IntendedFor fields to associate the fieldmaps with the BOLD files?

Best,
Steven

[erbenne]

no sir, they don’t–is this something Flywheel needs to correct, or is there a way to modify this on my end?

[Steven]

This is something you would need to correct on your end. You can add them manually to the files (or make a script to do this, see below for a quick example I made in python).

@Steven

Assumes there’s no ses-* level. Make bids the path to your BIDS root directory. You’ll have to change the definitions for fmaps_func_jsons and fmaps_dwi_jsons to include the proper search string to find the appropriate jsons. Also assumes that all fmri fmaps apply to all fmri niftis. If these assumptions aren’t correct for you hopefully there’s enough here that you can adapt to meet your needs.

import json
import os
import glob
bids = ''
subs = glob.glob(bids+'sub*')

for sub in subs:
    func_niis = [x.replace(sub+'/','') for x in glob.glob(sub+'/func/*.nii*')]
    dwi_niis = [x.replace(sub+'/','') for x in glob.glob(sub+'/dwi/*.nii*')] 
    fmaps_func_jsons = glob.glob(sub+'/fmap/*fMRI*.json')
    fmaps_dwi_jsons = glob.glob(sub+'/fmap/*dwi*.json')
    for file in fmaps_func_jsons:
        with open(file) as f:
            data = json.load(f)
        IF = {"IntendedFor":func_niis}
        data.update(IF)
        with open(file, 'w') as outfile:
            json.dump(data, outfile,indent=2,sort_keys=True)
    
    for file in fmaps_dwi_jsons:
        with open(file) as f:
            data = json.load(f)
        IF = {"IntendedFor":dwi_niis}
        data.update(IF)
        with open(file, 'w') as outfile:
            json.dump(data, outfile,indent=2,sort_keys=True)

[erbenne]

Ok awesome, thank you so much!!