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update aim1 and aim2 modeling#6

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henrymj wants to merge 231 commits intopoldracklab:masterpoldracklab/Self_Regulation_Ontology_fMRI:masterfrom henrymj:masterhenrymj/Self_Regulation_Ontology_fMRI:masterCopy head branch name to clipboard

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Commits on Dec 5, 2019

• add script to create fsl ppi events

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Commits on Jan 21, 2020

• update event regressor modeling

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Commits on Jan 24, 2020

• convert 1stlevel_analysis.ipynb to .py

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• singularitize

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• reverting to old commit that was overwritten

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• Merge branch 'master' of https://github.com/mckenziephagen/Self_Regulation_Ontology_fMRI

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• removed stray lines

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• Merge branch 'master' into master

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• add back a_comp_cor flag

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• Merge pull request #2 from mckenziephagen/master

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• merging henry with master

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• a_comp_cor 1st_level notebook

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• still fixing merge

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• fix merge conflict?

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• a_comp_cor notebook

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• Merge branch 'master' of https://github.com/henrymj/Self_Regulation_Ontology_fMRI

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Commits on Feb 4, 2020

• create design_matrix scripts

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Commits on Feb 7, 2020

• add repo to sherlock, improve visuals

  

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• remove trial regressor, add parametrics

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• fix gitignore issue

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• scale timeseries plotting

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• plot truncated timeseries

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• streamline slurm visualization files

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• add WATT practice regressor

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• correct discountFix junk modeling

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Commits on Feb 13, 2020

• update regressors, 1st level contrasts

  

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• updated 2ndlevel fmriprep path

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• update 2ndlevel mask paths

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Commits on Feb 18, 2020

• demean parametric regressors

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Commits on Feb 19, 2020

• add interaction example

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• old analysis

  

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• fix first level conflict

  

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• add time series parcellation

  

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• add WATT trial regressor

  

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Commits on Feb 21, 2020

• create simple&readable event files

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• drop index on simplified_events.csv

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Commits on Mar 2, 2020

• organize for 2ndlevel group contrasts

  

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Commits on Mar 6, 2020

• add code that creates simplified event files

  mckenziephagen

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Commits on Mar 11, 2020

• Merge branch 'master' of https://github.com/henrymj/Self_Regulation_Ontology_fMRI

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Commits on Mar 12, 2020

• comment 2ndlevel design matrix

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• update parcelation and alaysis

  

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Commits on Mar 13, 2020

• separate parcellation, improve Group 2ndLevels

  

  Henry Jones

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• update 2ndlevel ctask visualizations

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• add 2ndlevel vis batch files

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• correct 2ndlevel vis task array

  

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Commits on Mar 16, 2020

• allow nonuse of a_comp_cor flag

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• create noaCompCorr batch files

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Mar 17, 2020

• fix 2ndlevel visualization slices

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Commits on Mar 18, 2020

• use fd_stats.ipynb

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Commits on Mar 19, 2020

• prepare for new demeaning paradigm

  henrymj

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• use multiple sherlock partitions

  

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• merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Mar 20, 2020

• prepare for group visualizations

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• use new demeaning

  

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Commits on Mar 25, 2020

• return demeaned list not array

  

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• try new CCTHot regressors

  

  Henry Jones

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Commits on Apr 14, 2020

• start with impoverished models

  

  Henry Jones

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• update group_RTs via ipnb

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Commits on Apr 21, 2020

• fix impoverished models

  

  Henry Jones

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• fsl BET batchfile-ation

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• setup fsl DPX template eg

  

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• practice DPX fsl batch files

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Commits on Apr 22, 2020

• reorganize fsl dirs

  

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• test run_DPX_FEAT.sh

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• update DPX bash

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• reorganize fsl dirs

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• run DPX FEAT

  

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• create aim1 task FEAT.sh files

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• add TOT_VOX, declutter

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Commits on Apr 23, 2020

• corrct FSL run shs

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• add time to batch files

  henrymj

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• boolify fsl RT regressor

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• update fsl run scripts for RT

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• stash template batch change

  

  Henry Jones

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• stash

  

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• make task first level FEAT fsf'f

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Apr 30, 2020

• fixes correct column for stop/motor stop on stop trials

  mckenziephagen

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• Merge pull request #3 from mckenziephagen/master

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Commits on May 29, 2020

• exclude nodes 1&2

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• add do over DPX subjects

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• increase time limit

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Commits on Jun 12, 2020

• add fsl 2ndlevel scripts

  

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• add DPX RT-True 2ndlvl

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Commits on Jun 15, 2020

• add RT-True and negative contrasts

  

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Commits on Jun 17, 2020

• task timelocked resps

  

  Henry Jones

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• organize aim1 network qc

  henrymj

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• run network notebook

  

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• batch running of timelock

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Commits on Jun 18, 2020

• work on timelock

  

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• allow for trials w/ <num_TRs to be timelocked

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• DPX timelocked responses

  

  Henry Jones

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• correct network analyses

  

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• prepare for all task timelock

  

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• run timelocking analysis

  

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Commits on Jun 19, 2020

• comment timelocking script

  henrymj

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Commits on Jul 17, 2020

• add aim1 EFA notebooks

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Commits on Jul 28, 2020

• try EFA params

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• prepare 2ndlevel design matrix

  henrymj

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• remove failed timeseries analysis

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Jul 29, 2020

• add 2ndlevel confounds

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• fix 2ndlevel confound path issues

  

  Henry Jones

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• drop NaNs from 2ndlevel desMat, maps

  henrymj

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

  henrymj

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Commits on Aug 7, 2020

• attempt noFD 2ndlevel design matrix

  

  Henry Jones

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Commits on Sep 1, 2020

• use tensorflow for parcellations

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• clean util files, simplify WATT events

  henrymj

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• flake analysis scripts

  henrymj

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• compute accuracy scores for mac and friends

  henrymj

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• resolve conflicts in analysis scripts

  henrymj

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• fix typo

  

  Henry Jones

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• accept incoming changes

  

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• drop pickle import

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• flake firstlevel_utils.py

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• flake 2ndlevel_utils

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Commits on Sep 2, 2020

• add AROMA functionality?

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Commits on Sep 3, 2020

• disable 2ndlevel DMs

  henrymj

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• add informative print statements

  henrymj

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• attempt quick fix of mask issue

  henrymj

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Commits on Sep 4, 2020

• investigate group mask with prints

  henrymj

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Commits on Sep 14, 2020

• implement rastko's mean mask fix

  henrymj

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Commits on Sep 15, 2020

• prepare to run all tasks

  henrymj

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Commits on Oct 1, 2020

• w fmriprep20.2, change confounds_regressors to confounds_timeseries

  henrymj

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Commits on Oct 7, 2020

• drop owners nodes for vis

  henrymj

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Commits on Oct 9, 2020

• prepare to rerun second levels with age and sex regressors

  henrymj

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Commits on Oct 12, 2020

• update visualizer to save THE CORRECT PLOTS

  henrymj

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• update naming for visualization plots

  henrymj

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• fix plotting typo

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Commits on Oct 13, 2020

• add ability to plot pvals through neg log10 transform

  henrymj

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• add p-masked masked visualizations

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Commits on Oct 23, 2020

• accept rasko's nuisance regressors, change randomise call (tfce, c_threh)

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Commits on Oct 27, 2020

• attempt turning off demeaning of randomise

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• start a useful README for rerunning analyses

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Commits on Oct 28, 2020

• invert p files (1 - p) to fix fsl disp kink

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Commits on Oct 29, 2020

• rename plot utils, include VIF plot, symlink notebook utils for synchrony

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Commits on Nov 24, 2020

• add simulation notebooks, update WATT events

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• fix watt event subset strs?

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Commits on Nov 25, 2020

• flake event_utils.py

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• add junk conversion for WATT

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Commits on Nov 30, 2020

• add time for WATT visualizations

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• update CCTHot to appropriately capture trial-length regressors

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• improve get_ev_vars data type handling

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• update durations to meanRT within run for regressors

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• update event utils to use meanRT

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Commits on Jan 20, 2021

• first attempt at adding 2ndlevel meta json

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Commits on Jan 31, 2021

• add RT to 2ndlvl DMs

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Commits on Feb 1, 2021

• change rstrip to replace to fix contrast names

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Commits on Mar 2, 2021

• prepare new CCTHot regressors along with minor sourcery cleanup

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Commits on Mar 3, 2021

• disable CCTHot Button Press regressors

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Commits on Mar 4, 2021

• drop button press regressors from CCTHot contrast

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• save out new firstlevel maps

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Commits on Mar 18, 2021

• update second levels for proper randomise call, RT contrasts

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• flatten assignment then use of rt_cols in randomise

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• update singluarity path to version with updated nipype for multiple f-tests

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• import first_level_metas for 2ndlevel DM

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• streamline 2ndlevel demeaning

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• fix contrast list of tuples parens issue

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Commits on Mar 19, 2021

• use columns.get_loc to confirm contrast location in list

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• add des_mat in call to randomise, simplify desMat building function

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• change des_contrasts from tuple to list for appending in randomise, fix rt_neg contrast label

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• lengthen 2ndlevel jobs for more permutations moving forward

  

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• sourcery refactor file context in firstlevel_utils

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• standardize RT capitalization for meta dicts

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• support >1 digits in randomise outputs for name mapping

  henrymj

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• separate singularity configs for 1st and 2nd levels

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Commits on Mar 20, 2021

• fix 2ndlevel singularity paths to new nipype image

  

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Commits on Mar 22, 2021

• update parcellation script and job file for easier reading, editing

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• modify beta parcellation scripts to work with new py3-env

  

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Commits on Mar 24, 2021

• streamline visualizations for new 2ndlevels with f-tests

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• update visualization scripts to run on sherlock, threshold p-files

  

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• remove RT+cti from two_by_two metadata, simplify its second levels

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Commits on Mar 30, 2021

• update visualizations to standardize names, include neg t-tests

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• switch to tfce randomise call, change randomise output sctructure to keep des files

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Commits on Mar 31, 2021

• update visualizations to handle new randomise output structure

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• fix vis script to work on sherlock

  

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• save out randomise call for the future

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• update visualizations to ignore f-files, use t-pvals as thresh

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Commits on Apr 2, 2021

• fix nipype --fonly flag, prepare for f-tests for 2ndlevels

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Commits on Apr 3, 2021

• scale up to 10k perms and separate out intercept and RT models

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• include scnd_lvl flag in job,file titles for clarity

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Commits on Apr 5, 2021

• try to parallelize scnd_lvl RT analyses

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• update vis script for intercept results, separate randomise outputs

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Commits on Apr 6, 2021

• add time for perms for 2ndlevels, fix path issue for RT 2ndlevels

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Commits on Apr 9, 2021

• add SUIT atlas for Mac Et Amis

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• for parcels,fix contrast naming, add SUIT call

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• drop parcel_loc command, deprecated

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• drop parcel loc arg. focus on SUIT parcel for beta_parcel

  

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• change SUIT atlas path for parcel script

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• make atlas path absolute for parcellation

  

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• introduce atlas_dir path for local atlases

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Commits on Apr 12, 2021

• allow 2ndlevels to continue where they left off if incomplete

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• fix up beta_parcellation script to work on sherlock, change batch to finish of SUIT parcellation

  

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Commits on Apr 15, 2021

• separate DPX RT regressors to capture unique variance

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Commits on Apr 19, 2021

• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Apr 22, 2021

• add RT contrasts to DPX

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on Apr 27, 2021

• update WATT contrast list for maps

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• add motorStop RT contrasts for maps

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on May 6, 2021

• add code for regressing physio from rest

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• fix paths to physio files, print statements

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• specify fw_dir from args in physios script

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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Commits on May 7, 2021

• update flywheel data path for physio regression

  

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• change common slice onset for aim1 physio regression

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• fix argparse typo

  

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Commits on May 10, 2021

• add rest timeseries parcellation, tweak beta parcellation script

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Commits on May 11, 2021

• setup scripts to make 4d images

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Commits on May 14, 2021

• use AROMA denoised images for physio regression

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Commits on Jun 1, 2021

• add newest notebooks for prereg analyses

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Commits on Jun 25, 2021

• Created a requirements.txt to create a conda env for EFA

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Commits on Aug 23, 2021

• update README to provde clarity on replication

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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• remove Ian's notes on env/img in root README

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Commits on Aug 25, 2021

• Update firstlevel_utils.py

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• Update 1stlevel_analysis.batch

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• update mode for repo

  

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• Merge branch 'master' of github.com:henrymj/Self_Regulation_Ontology_fMRI

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