tvb-ukbb
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McIntosh-Lab
TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
Issue: Pull request shows commits that have already been brought over
Tract length matrices differ depending on probtrackx implementation (GPU, GPU batch, CPU, CPU batch)
There is only ~ 0.66 correlation between tract length matrix outputs (for the same input data) of the pipeline's various probtrackx options: GPU, GPU batch, CPU, CPU batch. This suggests...
1. update main branch with ADNI reparcellation tool 2. update wiki documentation re: reparcellating only on subject run with a version of the pipeline that is reparcellation-capable (post-reparcellation tool commit)....
Currently, toggling the GPU flag off in init-vars may produce errors due to commands for which we have not provided CPU alternatives (e.g. eddy_cuda in bb_eddy_wrap). Other potential errors have...
Things to clean up: - [ ] subject directory variable naming conventions (e.g., $subjdir, $direc, $baseDir are all used to mean the same directory) - [ ] turn off verbose...
Not sure if we need it since we provide an installer and container. Also need to determine if just testing the pipeline on a couple of subjects is sufficient when...
This is a behaviour of AFNI's 3dROIMaker that we need to account for. From the 3dROIMaker documentation (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dROIMaker.html): > If an INSET ROI has no corresponding REFSET label, then the...
UKBB pipeline comes with UKBB-specific [template](https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/master/templates/template_GM.nii.gz) which is what is currently being called by [VBM](https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/3cebec9f0d26ddfb75b82ea7b5ae678a770eb505/bb_structural_pipeline/bb_vbm#L38) Need to develop some code to create study-specific template ahead of time; see FSL documentation...
will require dataset-specific customization of the code here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/master/bb_pipeline_tools/bb_UKBB_to_BIDS_converter.py
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TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline