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nih-fmrif / code-convergence-summaries

Repo for writing progress reports from the DCCC AFNI hackathon in Sept, 2018
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Replacing MCFLIRT with 3dVolReg in FMRIPREP #2

Open chrisgorgo opened 6 years ago

chrisgorgo commented 6 years ago

Project Title

Replacing MCFLIRT with 3dVolReg in FMRIPREP

Contributors

Name Position Institute
Chris Gorgolewski Co-Director Stanford Center for Reproducible Neuroscience

Many thanks to Chris Markiewicz and Bob Cox for comments and feedback.

Project Summary

Understand how AFNI is saving affine matrices and using this knowledge to replace MCFLIRT with 3dVolReg in FMRIPREP

Project Significance

Understanding affine matrix file format used in AFNI will be useful in context of the upcoming effort to design a universal format for storing transformations. In context of FMRIPREP being able to choose between MCFLIRT and 3dVolReg gives us more options.

Progress Report

Functions to convert between AFNI and ANTs affine transformation files In person interactions are still the most effective way to get all the necessary information.

Project URLs

https://github.com/poldracklab/fmriprep/pull/1283#pullrequestreview-155495048

yarikoptic commented 6 years ago

You could add to significance the license aspect for choosing between FSL ( non-free -- couldn't be used in commercial settings without paying etc) and AFNI

ruyuanzhang commented 5 years ago

I am new to fMRIprep and still looking for functions that can convert AFNI affine matrics to FSL matrics. But after I read this conversation I am still lost.. Can someone point me to the function in fmriprep?? Thanks

mb3152 commented 2 years ago

I know this issue is very old, but echoing the concerns of @yarikoptic, it would be great to run fMRIPrep without FSL, and the most obvious first step would be to replace MCFLIRT with 3dVolReg. Is there still momentum to do this?