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MASILab / Synb0-DISCO

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps
https://my.vanderbilt.edu/masi
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Missing b0_all.nii.gz with --notopup flag #66

Closed ivonnecruz closed 12 hours ago

ivonnecruz commented 1 month ago

Hi! I’m working with a dataset that doesn't use reverse encoding (60 dir, b = 1000, PE-dir = j-). Recently, I was exploring Synb0-DISCO to obtain b0_all.nii.gz and use it in a customized version of eddy/topup. However, when I use the --notopup flag, I don’t find the b0_all.nii.gz file in the outputs folder.

sudo docker run --rm \
-v $(pwd)/INPUTS/:/INPUTS/ \
-v $(pwd)/OUTPUTS:/OUTPUTS/ \
-v /usr/local/freesurfer/7.4.1/license.txt:/extra/freesurfer/license.txt \
--user $(id -u):$(id -g) \
leonyichencai/synb0-disco:v3.0 \
--notopup

SYNB0_outputs

I’m wondering if I can obtain the equivalent of b0_all.nii.gz by concatenating b0_d_smooth.nii.gz and b0_u.nii.gz. I tried this command: fslmerge -t b0_all.nii.gz b0_d_smooth.nii.gz b0_u.nii.gz

It's important to mention that I am working with Windows Subsystem for Linux (WSL 2, Windows 10, Ubuntu 22).

Any suggestion is welcome. Thanks!

schillkg commented 2 weeks ago

Thank you for opening this issue, we should mention this in our README. You can indeed run:

fslmerge -t /OUTPUTS/b0_all.nii.gz /OUTPUTS/b0_d_smooth.nii.gz /OUTPUTS/b0_u.nii.gz

This is how we do it internally within the container, and should results in an image that is ready for topup-like processing.