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New script dwicat #1626

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merged 2 commits into from Jun 18, 2019

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@jvohryzek
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commented Jun 8, 2019

Hey Robert,
Could you get it approved by some other developer.

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Lena & Jakub

New script dwicat
Co-authored-by: Lena Dorfschmidt <ld548@cam.ac.uk>
Co-authored-by: Robert E. Smith <robert.smith@florey.edu.au>

@Lestropie Lestropie added the scripts label Jun 8, 2019

@Lestropie Lestropie self-assigned this Jun 8, 2019

@Lestropie Lestropie marked this pull request as ready for review Jun 8, 2019

dwicat: Give 4D b=0 images to mrhistmatch
Enabled by changes in #1628

Provide all b=0 volumes of each input series to mrhistmatch, rather than explicitly calculating the mean b=0 image. This provides a greater amount of data for the least squares determination of scaling factor between series. This was however not possible prior to #1628, as previously mrhistmatch worked explicitly on 3D images only.

@Lestropie Lestropie requested a review from jdtournier Jun 8, 2019

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commented Jun 8, 2019

Closes #1428.

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Looks great, thanks!

My one comment (based on a recent discussion where this functionality will be most welcome) would be to add an option to set the average b=0 intensity - useful in cases where the data might come from different scanners where the scaling might differ wildly between subjects. But it's nothing that can't be done in a subsequent step, so don't let that stop this from merging.

@jdtournier jdtournier merged commit 5cb2397 into MRtrix3:dev Jun 18, 2019

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commented Jun 25, 2019

Manually setting average b=0 intensity would be pretty easy. What I actually wanted to do here, but couldn't convince myself that my math was correct, was to intensity-match all protocols to all other protocols, producing a scaling factor matrix, and then scale each protocol individually in such a way as to converge their intensities toward a common target, rather than arbitrarily using the first scan as the "target" intensity.

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