Important Update: Bug Fix in CBIG_preproc_fslmcflirt_outliers for multi-echo cases

[Aihuiping Xue]

Dear CBIG Repository Users,

We would like to bring your attention to a recently identified bug in the  CBIG_preproc_fslmcflirt_outliers step of our preprocessing pipeline for multi-echo data.

The impact of the bug is as follows:

1. Single-echo cases: No impact.
2. Multi-echo cases: The impact depends on your workflow:
   i. If you run the CBIG_preproc_spatial_distortion_correction step immediately after CBIG_preproc_fslmcflirt_outliers, your results are not affected.
   ii. If you did not run the CBIG_preproc_spatial_distortion_correction step immediately after CBIG_preproc_fslmcflirt_outliers, the motion correction for the first echo remains correct, however, the transformation matrices applied to subsequent echoes are misaligned by one frame. 

While this issue is unlikely to have a major impact on most analyses, we strongly recommend updating your CBIG repository to the latest version and re-running preprocessing for your datasets if your workflow is affected.

If you are unsure whether your preprocessed data were affected, please send us your preprocessing config file to confirm.

How to update your CBIG Repository

We have pushed a release to the public repository. Please follow the instructions below to update your local repo. 

1. If you previously cloned or forked our public repo (https://github.com/ThomasYeoLab/CBIG), you need to update the repo by running:

cd $CBIG_CODE_DIR
git checkout master
git pull origin master

2. If you previously **cloned** our private repo (https://github.com/YeoPrivateLab/CBIG_private), i.e., Level-1 user of our private repo, you need to do:

cd $CBIG_CODE_DIR
git checkout develop
git pull upstream develop

We sincerely apologize for any inconvenience this may have caused and appreciate your understanding.

Best Regards,
CBIG lab