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brainlife / app-dtiinit

Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1
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Make t1 optional #3

Open soichih opened 6 years ago

soichih commented 6 years ago

According to dtiInit, t1 can be an optional input file

%   twFileName    = T1-weighted anatomical image. By default the diffusion
%                   data are aligned to this image. You can, however, pass 
%                   in the string 'MNI' to align the data to the standard

We could... 1) Make t1w optional 2) If user doesn't specify, pass string "MNI" to the t1FileName parameter.

soichih commented 6 years ago

@francopestilli Should we do this? Does it add value to our users?

francopestilli commented 6 years ago

I would prefer not to. DWI would lose the alignment with freesurfer

soichih commented 6 years ago

For most of our pipeline, yes we will need to align it to t1. But I thought that user might want to align it to MNI to do other analysis - maybe like comparing tracts across multiple subjects? We can also set the "tag" of the output datasets to show which coordinate systems the dwi is aligned to - to avoid misalignment issue.

btw.. I just opened https://github.com/brain-life/warehouse/issues/210 I think alignment information needs to be stored in more explicit way on BL.. but I could be overthinking.

francopestilli commented 6 years ago

OK if we rethink alignment then we can discuss this.