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brainlife / app-dwi2t1-nonlinear

App for running mrtrix3 dwipreproc and then performing nonlinear registration of dwi to T1 (by running ANTs affine+nonlinear registration of CSF masks of mean b0 and T1). Bvectors are rotated with the affine transform. App is recommended for bringing dwi to T1 space if no phase encoding contrast between b=0 images was collected (so mrtrix3 dwipreproc cannot perform inhomogeneity field estimation).
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App failing to find an input file #1

Open soichih opened 6 years ago

soichih commented 6 years ago 
TotalReadoutTime and PhaseEncodingDirection BIDS fields reqd to run mrtrix3 dwipreproc. Missing for ../5bc0d5876593aa002aeb8c4d/5967bffa9b45c212bbec8956/dwi.nii.gz
kathrynalpert commented 6 years ago

That's an expected error message if the dwi json doesn't contain fields that are needed for mrtrix3 dwipreproc

kathrynalpert commented 6 years ago

I could make the preprocessing an option, so a user could input his own preprocessed dwi. Is there any way to determine if a dwi input has the "preprocessed" tag?

soichih commented 6 years ago

Ah ok.. I should've read the error message more carefully. I need to make sure our datasets has those fields.

giulia-berto commented 3 years ago

hello, has this issue ever been resolved? I am running into the exact same error. Also, is the app supposed to work with both multi-shell and single-shell data?