Comments (2)
Some points to update:
- in the code main_conn_pipeline.sh is named sample_main.sh, need to make names consistent between code and documentation.
- Should clarify things like 'module' in the readme are specific to the IU supercomputing system and are not general instructions.
- is pip install dipy --user necessary? the text only describes two packages that are needed.
- maybe add the clarification that the config script must be pointed to in the main script if it is copied elsewhere and/or renamed.
- Add a clarification that main.sh must have executable permissions (which can go away if the file is copied elsewhere).
- Clearly state that the main script must stay in and be executed from the pipeline directory. The config file I think can be moved as long as its accurately pointed to in the main (line47) script.
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README will be redone as the bidsywork branch becomes master.
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Related Issues (20)
- minor edit: move a flag HOT 1
- organizational question: betQC brain
- Comment: Brain stem in brain mask HOT 1
- User provided subcortical parcellation boundary problem
- Issue: subcortical parcellations spreading into the cortex
- Cortical parcellation in the cerebellum
- comment: CSFvent parc in config HOT 1
- feature request: change or add a function version of main.sh HOT 1
- Dicom file checks do not follow directory links HOT 1
- Test Data transfer times
- Test running ConnPipe on various systems HOT 1
- Deprecation warning fo python get_data() HOT 1
- Find alternatives to saving data in .mat format HOT 1
- User-defined subcortical parcellation is not being used HOT 1
- Handle various cases for multiple EPI and Field Map sessions. HOT 1
- Handle BIDS data format with source and raw directories read-only
- changing parcellations after T1_B has been run HOT 1
- nuisasnce regression folders being created even if nuisance regression is set to false
- redundant rT1_brain_dof6_brr.nii.gz generation
- path_DWI_EDDY variable needs rename to EDDYpath in line 89 and 90 of DWI_A_eddy.sh
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