PyBASC

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Affinity threshold list, blocklength list, and cluster methods should be all made into iterables at the individual level. If user specifies say 2 thresholds, 2 block lengths, and 2 cluster...

AkiNikolaidis

Output folders in --parallelized too long

1

I think it would be better to make all the outputs immediately available in the first folder, instead of making them so deeply nested. I realize it's not as flexible...

AkiNikolaidis

Seems that when running on larger datasets- join group stability memory load is quite high, and so when running in parallel can overwhelm the computer

AkiNikolaidis

- [ ] If it passes the tests: - [ ] Version bump - [ ] Build package - [ ] Upload to Pypi

anibalsolon

Hey @AkiNikolaidis https://github.com/AkiNikolaidis/PyBASC/blob/master/PyBASC/basc.py#L47 At this line, shouldn't the subjects be normalized individually before concatenating them?

anibalsolon

Give a worst-case estimation for nodes `estimated_memory`, so nipype can better schedule the resources.

anibalsolon

When a workflow is completed, some of the outputs are created twice. For example the group_stability_matrix.npz is saved within workflow_output/group_stability_matrix and within workflow_output/basc_workflow_runner/basc/join_group_stability Many other files are saved both in...

AkiNikolaidis

To keep here the idea, the `__main__.py` `run_PyBASC` function could be one call to the pipeline, passing the lists of parameters so the whole parameters combinatory can be parallelized throug...

anibalsolon

What input params need to be changed to get this running? ``` def basc_run(subjects_list, basc_config): import os import numpy as np import nibabel as nib import yaml from basc.basc_workflow_runner import...

dPys

Test_basc.py functions missing fail cases: * Generate Blobs * Generate_simple_blobs * Generate_blobs_3d * Test_cluster_timeseries * Test_individual_stability_matrix * Test_cross_cluster_individual_stabiltiy_matrix * Test_expand_ism_options * Test_data_compress_expand * Test_nifti_individual_stability * test_cluster_matrix_average * new_test_group_stability_matrix * test_group_stability_matrix...

AkiNikolaidis