Priebe edits #396
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Priebe edits #396
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Lawreros
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Jun 29, 2020
* Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * Update Dockerfile Fix dockerfile to take from deploy branch of neuroparc and m2g * Update m2g_func.py Add function descriptions
Lawreros
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Oct 19, 2020
* add warning about default seeding in tutorial (#378) Co-authored-by: Ross Lawrence <[email protected]> * Cpac addition (#395) * Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * Update Dockerfile Fix dockerfile to take from deploy branch of neuroparc and m2g * Update m2g_func.py Add function descriptions * add missing import * Fix reference error * Fix default pathing for mask files * Fix gen_tissue file issues when skipping reg * error * fix check error * oops * code doesn't work with fury >= 0.6 * issues with fury. just dont run ever * connectomes not generated? * Add check for parcellations * checking * a * Add parallel option for reading streamlines * add n_cpu to dwi pipeline * remove print lines * remove print lines * forgot self * change to int * try without profiler * try refactor * Fix parallel error finally * Move args outside main() Co-authored-by: Alex Loftus <[email protected]> Co-authored-by: j1c <[email protected]>
Lawreros
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Apr 4, 2021
* Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * first pass at converting cpac to py3 * update dockerfile with new libraries for cpac in python3 * Dockerfile changes for py3 * Update m2g_pipeline cpac settings file * remove keyerror for roi loss * add python2 back into dockerfile, fix gen_utils bug * update gen_utils with new function arguments and errors * have eddy_correct called in python2 environment * add virtualenv for eddy_correct * fix bug where edgelists start at 2 * add multiprocessing to connectome estimation * Bug fix (#401) * add warning about default seeding in tutorial (#378) Co-authored-by: Ross Lawrence <[email protected]> * Cpac addition (#395) * Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * Update Dockerfile Fix dockerfile to take from deploy branch of neuroparc and m2g * Update m2g_func.py Add function descriptions * add missing import * Fix reference error * Fix default pathing for mask files * Fix gen_tissue file issues when skipping reg * error * fix check error * oops * code doesn't work with fury >= 0.6 * issues with fury. just dont run ever * connectomes not generated? * Add check for parcellations * checking * a * Add parallel option for reading streamlines * add n_cpu to dwi pipeline * remove print lines * remove print lines * forgot self * change to int * try without profiler * try refactor * Fix parallel error finally * Move args outside main() Co-authored-by: Alex Loftus <[email protected]> Co-authored-by: j1c <[email protected]> * add parcellation selection for functional pipeline * fm2g bug fixes * fix entrypoint bug from setup.py * version-lock pybids * travis update test * travis fix * travis fix * add 4mm parcellation option * add aws pull * change pip to pip3.6 for travis * change aws call to be run in docker container * fix typo * update aws sync * functional pipeline update * fix tr-pulling bug * allow for 1+ functional files * add memory monitor to functional pipeline * add options for resource monitoring * add conversion of connectome to edgelist in func pipeline * include connectome conversion in functional pipeline * update dockerfile * Update README.md * fix upload bug for multiple functional subjects * version control fury and hyppo * update Co-authored-by: Alex Loftus <[email protected]> Co-authored-by: j1c <[email protected]>
Lawreros
added a commit
that referenced
this pull request
Nov 20, 2021
* Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * first pass at converting cpac to py3 * update dockerfile with new libraries for cpac in python3 * Dockerfile changes for py3 * Update m2g_pipeline cpac settings file * remove keyerror for roi loss * add python2 back into dockerfile, fix gen_utils bug * update gen_utils with new function arguments and errors * have eddy_correct called in python2 environment * add virtualenv for eddy_correct * fix bug where edgelists start at 2 * add multiprocessing to connectome estimation * Bug fix (#401) * add warning about default seeding in tutorial (#378) Co-authored-by: Ross Lawrence <[email protected]> * Cpac addition (#395) * Dockerfile edit * Add cpac-necessary libraries to Dockerfile * add initial functional pipeline scripts * fix typo * fix docker typos * fix cpac directory organization * add no-caching on pip installations and apt-get clean * adapt directorysweeper to handle fmri data, initial fmri pipeline funcitons added * initial working prototype of m2g_func_worker * add s3 push capabilities to functional pipeline * add input arguments for functional pipeline * add info to acquisition input argument * update m2g_cloud funcitons for new functional pipeline * typo fix * Update m2g_pipeline.yaml * change script to go up to 10 GB memory per participant * changes to cpac parameters to allow ec2 instances to function * add functional pipeline local batch running * ec2 test * remove memory limitation * add gigabyte control to f-pipeline * add n_cpu control * fix cpac terminal call typo * derek_changes * final configuration edits * add more specific parameters to crawl_bucket * Priebe edits (#396) * necessary changes to allow large parcellations to run * typo fix * typo fix * allow multiple parcellations to be run * add csv import * version lock cpac * Update Dockerfile Fix dockerfile to take from deploy branch of neuroparc and m2g * Update m2g_func.py Add function descriptions * add missing import * Fix reference error * Fix default pathing for mask files * Fix gen_tissue file issues when skipping reg * error * fix check error * oops * code doesn't work with fury >= 0.6 * issues with fury. just dont run ever * connectomes not generated? * Add check for parcellations * checking * a * Add parallel option for reading streamlines * add n_cpu to dwi pipeline * remove print lines * remove print lines * forgot self * change to int * try without profiler * try refactor * Fix parallel error finally * Move args outside main() Co-authored-by: Alex Loftus <[email protected]> Co-authored-by: j1c <[email protected]> * add parcellation selection for functional pipeline * fm2g bug fixes * fix entrypoint bug from setup.py * version-lock pybids * travis update test * travis fix * travis fix * add 4mm parcellation option * add aws pull * change pip to pip3.6 for travis * change aws call to be run in docker container * fix typo * update aws sync * functional pipeline update * fix tr-pulling bug * allow for 1+ functional files * add memory monitor to functional pipeline * add options for resource monitoring * add conversion of connectome to edgelist in func pipeline * include connectome conversion in functional pipeline * update dockerfile * Update README.md * fix upload bug for multiple functional subjects * version control fury and hyppo * update * test update Co-authored-by: Alex Loftus <[email protected]> Co-authored-by: j1c <[email protected]>
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