Reply To: Only do distortion correction

Forums Forums BrainSuite Diffusion Pipeline (BDP) Only do distortion correction Reply To: Only do distortion correction

#2018
sychoi
Participant

Hey Miguel,

1. Generally you should be fine to port it into other softwares. However, we can’t claim complete knowledge or responsibility over what is being done by other tools outside of BrainSuite so you will have to use your best judgement to figure out the right steps to take for your study.

2. It may be possible to use our registration-based distortion correction on BOLD images as the method is based on the physics of EPI distortion. However, applying this method on BOLD images has not been properly tested or examined by BrainSuite so we can’t make any guarantees on the performance. It’s absolutely worth giving it a try. The full description of the methods can be found here: Bhushan, Chitresh, et al. “Co-registration and distortion correction of diffusion and anatomical images based on inverse contrast normalization.” Neuroimage 115 (2015): 269-280.
You can find the source code for BDP here: http://forums.brainsuite.org/download/
or you can try to hack the command line tool by inputting dummy bvec and bval files, just making sure you have the right number of values to match the number of volumes in your BOLD images. Also at least one of the bvalues should equal to 0 since it the b=0 image is used as the reference image for the registration template.

If you give it a try, please let me know how it goes by replying on this thread. Very interested!

Good luck!