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Convert CPAC to Python3 version #403

Merged
merged 70 commits into from
Apr 4, 2021
Merged

Convert CPAC to Python3 version #403

merged 70 commits into from
Apr 4, 2021

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Lawreros
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Lawreros and others added 30 commits February 24, 2020 18:01
@Lawreros
Dockerfile edit
df96e2f
@Lawreros
Add cpac-necessary libraries to Dockerfile
4325abb
@Lawreros
add initial functional pipeline scripts
a9f56d8
@Lawreros
fix typo
974c583
@Lawreros
fix docker typos
cea1882
@Lawreros
fix cpac directory organization
b2760ca
@Lawreros
add no-caching on pip installations and apt-get clean
a888fae
@Lawreros
adapt directorysweeper to handle fmri data, initial fmri pipeline fun…
e321410 
…citons added
@Lawreros
initial working prototype of m2g_func_worker
4204f7f
@Lawreros
add s3 push capabilities to functional pipeline
55639c3
@Lawreros
add input arguments for functional pipeline
d5ea5f9
@Lawreros
add info to acquisition input argument
702d324
@Lawreros
update m2g_cloud funcitons for new functional pipeline
42fe199
@Lawreros
typo fix
3cb06e5
@Lawreros
Update m2g_pipeline.yaml
269581b
@Lawreros
change script to go up to 10 GB memory per participant
e57cb96
@Lawreros
Merge branch 'cpac-addition' of https://github.com/neurodata/m2g into…
c6ed04e 
… cpac-addition
@Lawreros
changes to cpac parameters to allow ec2 instances to function
c02509d
@Lawreros
add functional pipeline local batch running
6216a7c
@Lawreros
ec2 test
0bac703
@Lawreros
remove memory limitation
f000b26
@Lawreros
add gigabyte control to f-pipeline
3b41f93
@Lawreros
add n_cpu control
b449de3
@Lawreros
fix cpac terminal call typo
1e7255d
@Lawreros
derek_changes
8fc52ff
@Lawreros
final configuration edits
23dcbc1
@Lawreros
add more specific parameters to crawl_bucket
99f1b90
@Lawreros
Merge branch 'deploy' into cpac-addition
ba4492f
@Lawreros
Priebe edits (#396)
0d3dc42 
* necessary changes to allow large parcellations to run

* typo fix

* typo fix

* allow multiple parcellations to be run

* add csv import

* version lock cpac
@Lawreros
first pass at converting cpac to py3
31557ff
Lawreros and others added 29 commits October 26, 2020 22:50
@Lawreros
add parcellation selection for functional pipeline
0a2ca80
@Lawreros
fm2g bug fixes
ad46bb1
@Lawreros
Merge branch 'deploy' into cpac-py3
723800d
@Lawreros
fix entrypoint bug from setup.py
b1813e9
@Lawreros
version-lock pybids
db6afa5
@Lawreros
travis update test
63a7708
@Lawreros
Merge branch 'cpac-py3' of https://github.com/neurodata/m2g into cpac…
3eb4133 
…-py3
@Lawreros
travis fix
bf35ec8
@Lawreros
travis fix
aefbda9
@Lawreros
add 4mm parcellation option
65916e8
@Lawreros
add aws pull
6966600
@Lawreros
change pip to pip3.6 for travis
08c880b
@Lawreros
change aws call to be run in docker container
9487d30
@Lawreros
fix typo
e9fa451
@Lawreros
update aws sync
73c430c
@Lawreros
functional pipeline update
17a7768
@Lawreros
fix tr-pulling bug
a4a27b1
@Lawreros
allow for 1+ functional files
7a2a310
@Lawreros
add memory monitor to functional pipeline
e4ae587
@Lawreros
add options for resource monitoring
9d77bb3
@Lawreros
add conversion of connectome to edgelist in func pipeline
7a804d7
@Lawreros
include connectome conversion in functional pipeline
7169539
@Lawreros
update dockerfile
6e5e7c7
@Lawreros
Update README.md
7db6ff4
@Lawreros
fix upload bug for multiple functional subjects
f9742b0
@Lawreros
Merge branch 'cpac-py3' of https://github.com/neurodata/m2g into cpac…
2294438 
…-py3
@Lawreros
version control fury and hyppo
1d0f63f
@Lawreros
update
3cb845e
@Lawreros
Merge branch 'cpac-py3' of https://github.com/neurodata/m2g into cpac…
f551d4b 
…-py3
@Lawreros Lawreros merged commit 55499c7 into deploy Apr 4, 2021
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@Lawreros