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brainlife / app-dtiinit

Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1
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Auto detect "rotateBvecsWithCanXform", "rotateBvecsWithRx" parameters #1

Closed soichih closed 6 years ago

soichih commented 7 years ago

Currently, users have to select correct options for following paramters

"rotateBvecsWithCanXform": false,
"rotateBvecsWithRx": false,
"eddyCorrect": "-1"

I believe most users are not familiar with the first 2 parameters and we should explore ways to auto-detect these parameters if possible. @bcmcpher Do you know if there is a way to do that?

bcmcpher commented 7 years ago

I don't think there will be. This is a preprocessing decision people have to make. rotateBvecsWithCanXform() adjusts the bvecs with alignment to the T1 and rotateBvecsWithRx adjusts the bvecs during motion / eddy correction.

If we really don't want people manipulating them, they should just be locked on, honestly.

Brent

On Mon, Oct 9, 2017 at 11:02 AM, Soichi Hayashi notifications@github.com wrote:

Currently, users have to select correct options for following paramters

"rotateBvecsWithCanXform": false, "rotateBvecsWithRx": false, "eddyCorrect": "-1"

I believe most users are not familiar with the first 2 parameters and we should explore ways to auto-detect these parameters if possible. @bcmcpher https://github.com/bcmcpher Do you know if there is a way to do that?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/brain-life/app-dtiinit/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/ANRr_aDNaaW4aSWkEfm8-15RNNxPBxBjks5sqjV3gaJpZM4Pyn_y .

soichih commented 7 years ago

dtiInit's internal default for those parameters are both false, but @kitchell says that they almost always needs to be set to true - except for HCP project. So the defaults on this app are both set to true. To properly process HCP, user needs to flip it back to dtiInit's default (false).

If we can't automate this, we should do one or more of following.

1) Explain these parameters to death.. so that user can figure out what to do. Where to look, who to ask, etc.. 2) For projects that default option won't work (user needs to manually switch it back to false), then provide preprocessed dtiInit output so that user can just use the output. 3) Implement capability on Brain-Life to override the application defaults at project level. For example, iIf user tries to run app-dtiinit on HCP data, it will automatically set those options to false - by default.

I think we should do 1) first, then do either 2) or 3).

soichih commented 6 years ago

We now know that both of those bvecs flags should be set to true for HCP - without modifying the input bvecs like we used to. We've added a bit more description for those options as well. Closing.