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HCP Pipelines Improvements (ICAFIX, PostFix, RestingStateStats, TaskfMRIAnalysis, londitudinal/cross-sectional logic) #31

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HCP Pipelines Improvements (ICAFIX, PostFix, RestingStateStats, TaskfMRIAnalysis, londitudinal/cross-sectional logic) #31

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ce2c6db
first commit to github.umn.edu of bids apps hcppipeline app
tjhendrickson Mar 28, 2018
56f01cb
made changes to run.py in order to account for my BIDS infrastructure
tjhendrickson Mar 29, 2018
8f46b5b
last commit prior to removing branch
tjhendrickson Apr 3, 2018
53d615b
Added IntendedFor.py to create IntendedFor field if it does not exist…
tjhendrickson Apr 3, 2018
3b23b48
Merge branch 'dev' of github.umn.edu:hendr522/HCPPipelines into extend
tjhendrickson Apr 3, 2018
4f98e77
added IntendedFor scrit to run.py so it will take care of adding Inte…
tjhendrickson Apr 3, 2018
8ac3dad
changed run.py for Dockerfile implementation
tjhendrickson Apr 3, 2018
6c61788
added intendedfor script to run.py to add intendedfor field if it doe…
tjhendrickson Apr 6, 2018
bbab867
changed set_fieldmap with return_list=True to allow for multiple fiel…
tjhendrickson Apr 10, 2018
b91946f
merged changes from extend to allow for a list of fieldmaps
tjhendrickson Apr 10, 2018
4696caa
made changes to IntendedFor.py for user determined fudge factor betwe…
tjhendrickson Apr 10, 2018
197e040
added /bin/bash -c to entrypoint to fix bit set problem with udocker
tjhendrickson Apr 12, 2018
937bc62
fixed conflicts between local and remote branch
tjhendrickson Apr 12, 2018
35e86d3
remove entrypoint command so udocker will run
tjhendrickson Apr 12, 2018
ae79bb6
remove entrypoint command so udocker will run
tjhendrickson Apr 12, 2018
8b5e288
merged conflicts with master
tjhendrickson Apr 12, 2018
3f0c1ea
added diffusion pieces from jokedurnez fork commit 2c44cc0f6b
tjhendrickson Apr 12, 2018
6378f36
Added function to run ICA-FIX processing stream
tjhendrickson Apr 12, 2018
dc33ab0
install FIX along with dependencies to Dockerfile
Apr 13, 2018
5fbf323
added FIX along with dependencies such as R to dockerfile in order to…
tjhendrickson Apr 13, 2018
d52473d
added install for pcre for R install
tjhendrickson Apr 13, 2018
f47ac58
made several changes to download and incorporate FIX into container
tjhendrickson Apr 26, 2018
16861b9
created a TODO to determine input_file variable for ICAFIX
tjhendrickson Apr 26, 2018
fdc426f
ensure clean working tree
tjhendrickson Apr 27, 2018
ab32ac1
added v0.1 to master for versioning
tjhendrickson Apr 27, 2018
1cc0c75
added if-else statement to run pipelines when session labels are invo…
tjhendrickson May 1, 2018
5118fd3
changes made to run.py to ensure session label conditional would work
tjhendrickson May 1, 2018
eaead66
Merge branch 'extend' into master
tjhendrickson May 2, 2018
07d8b30
Merge pull request #2 from hendr522/master
tjhendrickson May 2, 2018
8b06f71
Finished writing ICAFIX portion of pipeline, can be tested
tjhendrickson May 2, 2018
1460c75
merged branch extend with master
tjhendrickson May 2, 2018
41efa1c
made changes within run.py so data outputted is owned by original use…
tjhendrickson May 3, 2018
47199c3
change how subject ID and how subject path is determined for session …
tjhendrickson May 3, 2018
64a75ba
added reptime variable so ICAFIX will work
tjhendrickson May 4, 2018
a189963
highpass variable was not being found, needed to change scope
tjhendrickson May 4, 2018
7bd1b56
changed if zooms and reptime statment
tjhendrickson May 4, 2018
cc17817
changed scope offmri processing call
tjhendrickson May 4, 2018
2275f9b
changed reptime to float
tjhendrickson May 4, 2018
2179add
made sure that output folders will be created if they don't exist alr…
tjhendrickson May 4, 2018
a16f9b3
changed DockerFile for singularity compatiability and updated version
tjhendrickson May 23, 2018
3c6f2ef
adding fsl_sub capability into image
May 29, 2018
0f83447
modified fsl_sub so queue names are generated
tjhendrickson May 29, 2018
36193db
added fsl_sub to DockerFile
tjhendrickson May 29, 2018
bf9ea23
changed environment variable FSL_FIX from opt/fix to /opt/fix so path…
tjhendrickson May 29, 2018
f396d16
changed R versions so FIX would run properly
tjhendrickson May 29, 2018
fbf253a
changed R versions so FIX would run properly
tjhendrickson May 29, 2018
31dbef0
ensured that dependencies were met to run PostFix (i.e. MCR version v81)
tjhendrickson May 29, 2018
d338bc8
Finished PostFix call within run.py. Execution testing needed. Began …
May 30, 2018
7bc3a05
remove SetUpHCPPipeline.sh from run.py
May 30, 2018
2890771
removed unneeded files and commented out sections in progress within …
tjhendrickson May 31, 2018
f27050f
changes to DockerFile so environment is set up correctly
tjhendrickson May 31, 2018
2c50592
made changes to run.py and DockerFile to include RestingStateStats
tjhendrickson Jun 1, 2018
3af4730
Delete mri_convert
tjhendrickson Jun 1, 2018
25ee198
Delete mri_convert.bin
tjhendrickson Jun 1, 2018
9401eed
Delete sources.sh
tjhendrickson Jun 1, 2018
dd20804
Delete SetUpHCPPipeline.sh
tjhendrickson Jun 1, 2018
4292ebc
Delete MCR_installer_input.txt
tjhendrickson Jun 1, 2018
873f47e
changed identation of posData within run.py
tjhendrickson Jun 1, 2018
cf17e6a
Merge branch 'master' of https://github.umn.edu/hendr522/HCPPipelines
tjhendrickson Jun 1, 2018
782df47
made changes to README.md to reflect current capabilities of release
tjhendrickson Jun 1, 2018
86e10e2
Update README.md
tjhendrickson Jun 2, 2018
943afa0
Update README.md
tjhendrickson Jun 2, 2018
856e95c
Update run.py
tjhendrickson Jun 2, 2018
b939175
playing around with R packages to meet FIX dependencies
tjhendrickson Jun 4, 2018
dd17549
finished testing of ICAFIX, RestingStateStats, and PostFix. Additiona…
tjhendrickson Jun 5, 2018
5401cc6
moved IntendedFor.py back to top level directory so it would run prop…
tjhendrickson Jun 6, 2018
8b5c071
removed pdb.set_trace() commands from run.py
tjhendrickson Jun 6, 2018
9ac1544
made a small change to run.py, for resting state processing use fmrin…
tjhendrickson Jun 6, 2018
a8675c3
finish out session label vs subject label if else condition. Addition…
tjhendrickson Jun 7, 2018
35cbd7d
session label logic was incorrect resulting in failed processing for …
tjhendrickson Jun 7, 2018
ad5fc48
created TaskfMRIAnalysis directory within container
Jun 11, 2018
156b66a
incremental progress on TaskfMRI implementation
tjhendrickson Jun 11, 2018
ce466ce
Reverted TaskfMRIAnalysis pipeline to v3.17.0
tjhendrickson Jun 12, 2018
23a4e6f
added generate_level1_fsf.sh to docker image
tjhendrickson Jun 12, 2018
2048ab4
place function and resting state underneath for loop
tjhendrickson Jun 14, 2018
0d40451
making sure odin repo is up to date
tjhendrickson Jun 15, 2018
2e3a4c9
backed out of user input section within intendedfor script
tjhendrickson Jun 18, 2018
3b1b3dc
added necessary features to generatefsf and TaskfMRIAnalysis. Still h…
tjhendrickson Jun 18, 2018
e67b1cd
added Singularity usage to README.md
tjhendrickson Jun 21, 2018
cec30da
resolved merge conflicts
tjhendrickson Jun 21, 2018
5a0b02f
removed TaskfMRIAnalysis and .idea
tjhendrickson Jun 21, 2018
6b0502d
correct merge conflict with Dockerfile
tjhendrickson Jun 21, 2018
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