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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

Commits on Dec 5, 2019

• add script to create fsl ppi events

  mckenziephagen

  committed
  ec08d37

Commits on Jan 21, 2020

• update event regressor modeling

  henrymj

  committed
  e29dae3

Commits on Jan 24, 2020

• convert 1stlevel_analysis.ipynb to .py

  henrymj

  committed
  1218a54

• singularitize

  henrymj

  committed
  0f40874

• reverting to old commit that was overwritten

  mckenziephagen

  committed
  cc912aa

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

  mckenziephagen

  committed
  5f0f61f

• removed stray lines

  mckenziephagen

  committed
  4d8466b

• Merge branch 'master' into master

  henrymj

  authored
  c87d591

• add back a_comp_cor flag

  henrymj

  committed
  42fce9a

• Merge pull request #2 from mckenziephagen/master

  Show description for e653738
  henrymj

  authored
  e653738

• merging henry with master

  mckenziephagen

  committed
  4ad6f4c

• a_comp_cor 1st_level notebook

  henrymj

  committed
  00d2510

• still fixing merge

  mckenziephagen

  committed
  46d8ce3

• fix merge conflict?

  henrymj

  committed
  6225d9a

• a_comp_cor notebook

  henrymj

  committed
  3ad7ac2

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

  mckenziephagen

  committed
  6d54b79

Commits on Feb 4, 2020

• create design_matrix scripts

  henrymj

  committed
  ff6d1cb

Commits on Feb 7, 2020

• add repo to sherlock, improve visuals

  

  Henry Jones

  committed
  2d817d3

• remove trial regressor, add parametrics

  henrymj

  committed
  b78cc10

• fix gitignore issue

  henrymj

  committed
  594fc95

• scale timeseries plotting

  henrymj

  committed
  a4319f8

• plot truncated timeseries

  henrymj

  committed
  e4a283b

• streamline slurm visualization files

  henrymj

  committed
  ce463c1

• add WATT practice regressor

  henrymj

  committed
  c55c93a

• correct discountFix junk modeling

  henrymj

  committed
  75b5b99

Commits on Feb 13, 2020

• update regressors, 1st level contrasts

  

  Henry Jones

  committed
  ae9fecd

• updated 2ndlevel fmriprep path

  henrymj

  committed
  2881cbe

• update 2ndlevel mask paths

  henrymj

  committed
  ee34185

Commits on Feb 18, 2020

• demean parametric regressors

  henrymj

  committed
  3b0cc3b

Commits on Feb 19, 2020

• add interaction example

  henrymj

  committed
  ec90e9d

• old analysis

  

  Henry Jones

  committed
  f24670e

• fix first level conflict

  

  Henry Jones

  committed
  e3acbc4

• add time series parcellation

  

  Henry Jones

  committed
  0eb11fe

• add WATT trial regressor

  

  Henry Jones

  committed
  c8292d7

Commits on Feb 21, 2020

• create simple&readable event files

  henrymj

  committed
  de020cb

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

  henrymj

  committed
  379ec4c

• drop index on simplified_events.csv

  henrymj

  committed
  ad78fa5

Commits on Mar 2, 2020

• organize for 2ndlevel group contrasts

  

  Henry Jones

  committed
  097742d

Commits on Mar 6, 2020

• add code that creates simplified event files

  mckenziephagen

  committed
  4ae009b

Commits on Mar 11, 2020

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

  mckenziephagen

  committed
  495a95d

Commits on Mar 12, 2020

• comment 2ndlevel design matrix

  henrymj

  committed
  34f049f

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

  henrymj

  committed
  569566c

• update parcelation and alaysis

  

  Henry Jones

  committed
  13996c4

Commits on Mar 13, 2020

• separate parcellation, improve Group 2ndLevels

  

  Henry Jones

  committed
  587556f

• update 2ndlevel ctask visualizations

  henrymj

  committed
  8b7873e

• add 2ndlevel vis batch files

  

  Henry Jones

  committed
  5c35d76

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

  Show description for 8171c88
  

  Henry Jones

  committed
  8171c88

• correct 2ndlevel vis task array

  

  Henry Jones

  committed
  eb72dcc

Commits on Mar 16, 2020

• allow nonuse of a_comp_cor flag

  henrymj

  committed
  a56b0ab

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

  henrymj

  committed
  7dadb0b

• create noaCompCorr batch files

  

  Henry Jones

  committed
  2df01ad

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

  Show description for 779da8a
  

  Henry Jones

  committed
  779da8a

Commits on Mar 17, 2020

• fix 2ndlevel visualization slices

  henrymj

  committed
  7730d32

Commits on Mar 18, 2020

• use fd_stats.ipynb

  henrymj

  committed
  8033803

Commits on Mar 19, 2020

• prepare for new demeaning paradigm

  henrymj

  committed
  730b58f

• use multiple sherlock partitions

  

  Henry Jones

  committed
  948c649

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

  Show description for 91c64fa
  

  Henry Jones

  committed
  91c64fa

Commits on Mar 20, 2020

• prepare for group visualizations

  henrymj

  committed
  186c5e5

• use new demeaning

  

  Henry Jones

  committed
  91497f5

Commits on Mar 25, 2020

• return demeaned list not array

  

  Henry Jones

  committed
  c9dadc5

• try new CCTHot regressors

  

  Henry Jones

  committed
  9f7e4c2

Commits on Apr 14, 2020

• start with impoverished models

  

  Henry Jones

  committed
  961ae55

• update group_RTs via ipnb

  henrymj

  committed
  4c283b5

Commits on Apr 21, 2020

• fix impoverished models

  

  Henry Jones

  committed
  3488ee2

• fsl BET batchfile-ation

  henrymj

  committed
  48eeffe

• setup fsl DPX template eg

  

  Henry Jones

  committed
  d834228

• practice DPX fsl batch files

  henrymj

  committed
  6a817e1

Commits on Apr 22, 2020

• reorganize fsl dirs

  

  Henry Jones

  committed
  f38c163

• test run_DPX_FEAT.sh

  henrymj

  committed
  495251e

• update DPX bash

  henrymj

  committed
  13cec12

• reorganize fsl dirs

  

  Henry Jones

  committed
  83cee69

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

  Show description for 22bb1f6
  

  Henry Jones

  committed
  22bb1f6

• run DPX FEAT

  

  Henry Jones

  committed
  bed9d37

• create aim1 task FEAT.sh files

  henrymj

  committed
  3e9552d

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

  henrymj

  committed
  6400e99

• add TOT_VOX, declutter

  henrymj

  committed
  c3edde3

Commits on Apr 23, 2020

• corrct FSL run shs

  henrymj

  committed
  a1e8a4e

• add time to batch files

  henrymj

  committed
  88889de

• boolify fsl RT regressor

  henrymj

  committed
  975db79

• update fsl run scripts for RT

  henrymj

  committed
  00b5785

• stash template batch change

  

  Henry Jones

  committed
  f876fe7

• stash

  

  Henry Jones

  committed
  dbe196e

• make task first level FEAT fsf'f

  henrymj

  committed
  bf5fb97

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

  Show description for 9942178
  

  Henry Jones

  committed
  9942178

Commits on Apr 30, 2020

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

  mckenziephagen

  committed
  2fec31c

• Merge pull request #3 from mckenziephagen/master

  Show description for 2b3ffcc
  henrymj

  authored
  2b3ffcc

Commits on May 29, 2020

• exclude nodes 1&2

  

  Henry Jones

  committed
  e8a38b3

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

  Show description for 8556935
  

  Henry Jones

  committed
  8556935

• add do over DPX subjects

  henrymj

  committed
  3975fbc

• increase time limit

  henrymj

  committed
  07c8e47

Commits on Jun 12, 2020

• add fsl 2ndlevel scripts

  

  Henry Jones

  committed
  2c2c622

• add DPX RT-True 2ndlvl

  henrymj

  committed
  214eaf1

Commits on Jun 15, 2020

• add RT-True and negative contrasts

  

  Henry Jones

  committed
  5cd8b14

Commits on Jun 17, 2020

• task timelocked resps

  

  Henry Jones

  committed
  256e2ff

• organize aim1 network qc

  henrymj

  committed
  bc05b4f

• run network notebook

  

  Henry Jones

  committed
  7c22ad4

• batch running of timelock

  henrymj

  committed
  b4dff32

Commits on Jun 18, 2020

• work on timelock

  

  Henry Jones

  committed
  9743f29

• allow for trials w/ <num_TRs to be timelocked

  henrymj

  committed
  938bd7d

• DPX timelocked responses

  

  Henry Jones

  committed
  4bba036

• correct network analyses

  

  Henry Jones

  committed
  bf164fd

• prepare for all task timelock

  

  Henry Jones

  committed
  fc3756f

• run timelocking analysis

  

  Henry Jones

  committed
  b53f1c8

Commits on Jun 19, 2020

• comment timelocking script

  henrymj

  committed
  71d87b6

Commits on Jul 17, 2020

• add aim1 EFA notebooks

  henrymj

  committed
  33c4fec

Commits on Jul 28, 2020

• try EFA params

  henrymj

  committed
  c2aec46

• prepare 2ndlevel design matrix

  henrymj

  committed
  5ee60ed

• remove failed timeseries analysis

  

  Henry Jones

  committed
  de1bd76

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

  Show description for 64db1ca
  

  Henry Jones

  committed
  64db1ca

Commits on Jul 29, 2020

• add 2ndlevel confounds

  henrymj

  committed
  fb6de3a

• fix 2ndlevel confound path issues

  

  Henry Jones

  committed
  b67d1ca

• drop NaNs from 2ndlevel desMat, maps

  henrymj

  committed
  b1892a1

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

  henrymj

  committed
  bd3cad4

Commits on Aug 7, 2020

• attempt noFD 2ndlevel design matrix

  

  Henry Jones

  committed
  a0a78f6

Commits on Sep 1, 2020

• use tensorflow for parcellations

  henrymj

  committed
  8fa62e8

• clean util files, simplify WATT events

  henrymj

  committed
  f897f46

• flake analysis scripts

  henrymj

  committed
  18e90c5

• compute accuracy scores for mac and friends

  henrymj

  committed
  9110ed7

• resolve conflicts in analysis scripts

  henrymj

  committed
  a6810e9

• fix typo

  

  Henry Jones

  committed
  99b8b1b

• accept incoming changes

  

  Henry Jones

  committed
  833793b

• drop pickle import

  henrymj

  committed
  14ac7e3

• flake firstlevel_utils.py

  henrymj

  committed
  f43ed5e

• flake 2ndlevel_utils

  henrymj

  committed
  5f2db8d

Commits on Sep 2, 2020

• add AROMA functionality?

  henrymj

  committed
  4a4ad14

Commits on Sep 3, 2020

• disable 2ndlevel DMs

  henrymj

  committed
  8a570ff

• add informative print statements

  henrymj

  committed
  c2ff34d

• attempt quick fix of mask issue

  henrymj

  committed
  9a1e2d0

Commits on Sep 4, 2020

• investigate group mask with prints

  henrymj

  committed
  ac1969f

Commits on Sep 14, 2020

• implement rastko's mean mask fix

  henrymj

  committed
  0653b52

Commits on Sep 15, 2020

• prepare to run all tasks

  henrymj

  committed
  0692776

Commits on Oct 1, 2020

• w fmriprep20.2, change confounds_regressors to confounds_timeseries

  henrymj

  committed
  8babfd4

Commits on Oct 7, 2020

• drop owners nodes for vis

  henrymj

  committed
  f09cb76

Commits on Oct 9, 2020

• prepare to rerun second levels with age and sex regressors

  henrymj

  committed
  c099117

Commits on Oct 12, 2020

• update visualizer to save THE CORRECT PLOTS

  henrymj

  committed
  5db62d9

• update naming for visualization plots

  henrymj

  committed
  8a43274

• fix plotting typo

  henrymj

  committed
  bb144d5

Commits on Oct 13, 2020

• add ability to plot pvals through neg log10 transform

  henrymj

  committed
  1b0df6a

• add p-masked masked visualizations

  henrymj

  committed
  db3e0fa

Commits on Oct 23, 2020

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

  henrymj

  committed
  bb33d96

Commits on Oct 27, 2020

• attempt turning off demeaning of randomise

  henrymj

  committed
  e553685

• start a useful README for rerunning analyses

  henrymj

  committed
  622a596

Commits on Oct 28, 2020

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

  henrymj

  committed
  1b87235

Commits on Oct 29, 2020

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

  henrymj

  committed
  ba62992

Commits on Nov 24, 2020

• add simulation notebooks, update WATT events

  henrymj

  committed
  2118a2f

• fix watt event subset strs?

  henrymj

  committed
  01cd559

Commits on Nov 25, 2020

• flake event_utils.py

  henrymj

  committed
  c0a961c

• add junk conversion for WATT

  henrymj

  committed
  42af32a

Commits on Nov 30, 2020

• add time for WATT visualizations

  henrymj

  committed
  cb11174

• update CCTHot to appropriately capture trial-length regressors

  henrymj

  committed
  7a56180

• improve get_ev_vars data type handling

  

  Henry Jones

  committed
  d6aa6f1

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

  Show description for 0f40c9e
  

  Henry Jones

  committed
  0f40c9e

• update durations to meanRT within run for regressors

  henrymj

  committed
  c2d2dc9

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

  henrymj

  committed
  3d13786

• update event utils to use meanRT

  henrymj

  committed
  b013b94

Commits on Jan 20, 2021

• first attempt at adding 2ndlevel meta json

  henrymj

  committed
  bc3522c

Commits on Jan 31, 2021

• add RT to 2ndlvl DMs

  henrymj

  committed
  e329f86

Commits on Feb 1, 2021

• change rstrip to replace to fix contrast names

  henrymj

  committed
  3d644a1

Commits on Mar 2, 2021

• prepare new CCTHot regressors along with minor sourcery cleanup

  henrymj

  committed
  26ba10e

Commits on Mar 3, 2021

• disable CCTHot Button Press regressors

  henrymj

  committed
  38bd988

Commits on Mar 4, 2021

• drop button press regressors from CCTHot contrast

  henrymj

  committed
  a8995c7

• save out new firstlevel maps

  henrymj

  committed
  9bb421b

Commits on Mar 18, 2021

• update second levels for proper randomise call, RT contrasts

  henrymj

  committed
  08754d2

• flatten assignment then use of rt_cols in randomise

  henrymj

  committed
  33bcc58

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

  henrymj

  committed
  a8d1f56

• import first_level_metas for 2ndlevel DM

  

  Henry Jones

  committed
  ab67f81

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

  Show description for 6a87cbc
  

  Henry Jones

  committed
  6a87cbc

• streamline 2ndlevel demeaning

  henrymj

  committed
  837109b

• fix contrast list of tuples parens issue

  henrymj

  committed
  de74b23

Commits on Mar 19, 2021

• use columns.get_loc to confirm contrast location in list

  henrymj

  committed
  e4d1e30

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

  henrymj

  committed
  102131c

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

  henrymj

  committed
  9907ec4

• lengthen 2ndlevel jobs for more permutations moving forward

  

  Henry Jones

  committed
  bfcc0f4

• sourcery refactor file context in firstlevel_utils

  henrymj

  committed
  48c07da

• standardize RT capitalization for meta dicts

  henrymj

  committed
  4f32a57

• support >1 digits in randomise outputs for name mapping

  henrymj

  committed
  b9ed2d8

• separate singularity configs for 1st and 2nd levels

  henrymj

  committed
  5d7d951

Commits on Mar 20, 2021

• fix 2ndlevel singularity paths to new nipype image

  

  Henry Jones

  committed
  13f4725

Commits on Mar 22, 2021

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

  henrymj

  committed
  698a7be

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

  

  Henry Jones

  committed
  b360dca

Commits on Mar 24, 2021

• streamline visualizations for new 2ndlevels with f-tests

  henrymj

  committed
  cc4e4d5

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

  

  Henry Jones

  committed
  7b600e5

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

  henrymj

  committed
  620a832

Commits on Mar 30, 2021

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

  henrymj

  committed
  bb38d39

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

  henrymj

  committed
  91abab4

Commits on Mar 31, 2021

• update visualizations to handle new randomise output structure

  henrymj

  committed
  4c81115

• fix vis script to work on sherlock

  

  Henry Jones

  committed
  ae88d58

• save out randomise call for the future

  henrymj

  committed
  2381751

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

  henrymj

  committed
  a9fa83a

Commits on Apr 2, 2021

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

  henrymj

  committed
  b61a553

Commits on Apr 3, 2021

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

  henrymj

  committed
  c368557

• include scnd_lvl flag in job,file titles for clarity

  henrymj

  committed
  85d8be2

Commits on Apr 5, 2021

• try to parallelize scnd_lvl RT analyses

  henrymj

  committed
  43fade8

• update vis script for intercept results, separate randomise outputs

  henrymj

  committed
  2bb1d2c

Commits on Apr 6, 2021

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

  henrymj

  committed
  d2ef254

Commits on Apr 9, 2021

• add SUIT atlas for Mac Et Amis

  henrymj

  committed
  508093a

• for parcels,fix contrast naming, add SUIT call

  henrymj

  committed
  d81d9eb

• drop parcel_loc command, deprecated

  henrymj

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  feb7f7d

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

  

  Henry Jones

  committed
  594fe56

• change SUIT atlas path for parcel script

  henrymj

  committed
  1c90f68

• make atlas path absolute for parcellation

  

  Henry Jones

  committed
  fc3a9e4

• introduce atlas_dir path for local atlases

  henrymj

  committed
  8475d63

Commits on Apr 12, 2021

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

  henrymj

  committed
  8d27b4f

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

  

  Henry Jones

  committed
  1d5d321

Commits on Apr 15, 2021

• separate DPX RT regressors to capture unique variance

  henrymj

  committed
  b24b0e8

Commits on Apr 19, 2021

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

  Show description for 539c900
  

  Henry Jones

  committed
  539c900

Commits on Apr 22, 2021

• add RT contrasts to DPX

  henrymj

  committed
  bacc3a3

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

  Show description for 4e0bc26
  

  Henry Jones

  committed
  4e0bc26

Commits on Apr 27, 2021

• update WATT contrast list for maps

  henrymj

  committed
  232ced1

• add motorStop RT contrasts for maps

  henrymj

  committed
  8cd94aa

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

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  Henry Jones

  committed
  5048969

Commits on May 6, 2021

• add code for regressing physio from rest

  henrymj

  committed
  4bd2310

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

  Show description for adbc931
  

  Henry Jones

  committed
  adbc931

• fix paths to physio files, print statements

  henrymj

  committed
  b556b4c

• specify fw_dir from args in physios script

  

  Henry Jones

  committed
  81e9c5f

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

  Show description for 0d3be2a
  

  Henry Jones

  committed
  0d3be2a

Commits on May 7, 2021

• update flywheel data path for physio regression

  

  Henry Jones

  committed
  2c20201

• change common slice onset for aim1 physio regression

  henrymj

  committed
  cac8b12

• fix argparse typo

  

  Henry Jones

  committed
  26d8861

Commits on May 10, 2021

• add rest timeseries parcellation, tweak beta parcellation script

  henrymj

  committed
  d38ccb7

Commits on May 11, 2021

• setup scripts to make 4d images

  henrymj

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  7d9ce8b

Commits on May 14, 2021

• use AROMA denoised images for physio regression

  henrymj

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  0d5bf37

Commits on Jun 1, 2021

• add newest notebooks for prereg analyses

  henrymj

  committed
  ca51bb0

Commits on Jun 25, 2021

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

  Rios-Jaime

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  a396910

Commits on Aug 23, 2021

• update README to provde clarity on replication

  henrymj

  committed
  4974db0

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

  henrymj

  committed
  833b1d8

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

  henrymj

  committed
  953a32f

Commits on Aug 25, 2021

• Update firstlevel_utils.py

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  bissettp

  authored
  910c79a

• Update 1stlevel_analysis.batch

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  bissettp

  authored
  c5515ff

• update mode for repo

  

  Henry Jones

  committed
  2e5f2e8

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

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  Henry Jones

  committed
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