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anthonyprinaldi wants to merge 233 commits intonightlyAICONSlab/MIRACL:nightlyfrom devAICONSlab/MIRACL:devCopy head branch name to clipboard

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Commits

Commits on Feb 27, 2024

• [fix] Change default atlas labels for ace reg to None

  Show description for 0db3290
  anthonyprinaldi

  committed
  0db3290

• [feature] Add vox and warp to single ace workflow

  anthonyprinaldi

  committed
  92562eb

• [fix] Add reg checker to single workflow

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  anthonyprinaldi

  committed
  15b39b4

• [fix] Clear reg dirs when overwrite

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  committed
  42202b1

• [feature] Add ability to skip segmentation

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  anthonyprinaldi

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  0a9e5ce

• [fix] Add seg skipping for single ace workflow

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  anthonyprinaldi

  committed
  11574c1

Commits on Feb 29, 2024

• [feature] Add percentile thresholding for conversion

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  anthonyprinaldi

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  863be85

Commits on May 1, 2024

• [feature] Add extreme value percentile correction to ACE

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• [wip] Update printing statement

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  3956999

• [wip] Try removing c3d data type conversion

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  0669d97

• [fix] Remove overwriting labels argument

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  971a483

• [fix] Update batch size and sw batch size

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  974dd76

• [feature] Chane MC flag to integer

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  446d2f7

• [fix] Move MC results to cpu

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  anthonyprinaldi

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  e34fcad

• [feature] Add GPU indexing for parallel running of ace workflow

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  bb9a2de

• [fix] Small bugfix for ensemble model

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  092b50c

• [fix] Change variable used in list comprehension

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• [fix] Overwriting val_outputs in loop

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• [fix] Remove print statements

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• [feature] Add option to skip conversion

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  5bdff24

• [fix] Add zero padding to the depth dimension of patches

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  a8d0e55

• [fix] Fix the calculation for the number of patches that fit in height and width

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• [feature] Add labels flag for warping clar to allen

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  22819dd

• [fix] Add logic to handle MC ACE models

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  1a32000

• [fix] Add check for None label in warp

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  76657f1

• [feature] Add hemi to ace heatmap

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• [feature] Add parser argument for binarization threshold of model output

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  39e3c57

• [fix] Create new arrays based on input size

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  630d048

• [feature] Add function for pvalue plotting

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  anthonyprinaldi

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  41427cd

• [feature] Add pvalue plotting to ACE

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  9bc71ac

• [fix] Update clusterwise script to work with half brain

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  d3d45b3

• [feature] Add json output to generate patches

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  5a5114d

• [fix] Change brain patch percentage saving to filename only

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  anthonyprinaldi

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  c1a7b55

• [feature] Add ace parser argument

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  3aaf8af

• [fix] Spelling mistake in ace flow parser

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  e48cec8

• [fix] Add detail to ace flow parser re-run options

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  0df7583

• [fix] Minor fixes to ace seg parser

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  anthonyprinaldi

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  48483c7

• [fix] Add more specific regex for registration checking

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  f22a761

• [fix] Update logic for handling atlas dir arg

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  0018b20

• [fix] Update os.getcwd() to Path.cwd()

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  a01f191

• [fix] Change pathlib operator

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  883df06

• [feature] Change order of ternary operators

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  d3e9160

• [feature] Add default value for mask argument

  anthonyprinaldi

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  9e0073a

• [fix] Change if logic to be more readable

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  7de40f6

• [fix] Use positive ternary operator

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  2ddf243

Commits on May 2, 2024

• [fix] Remove global variables

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  anthonyprinaldi

  committed
  5e00c5c

Commits on May 21, 2024

• [feature] Add instance segmentation to MIRACL

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  anthonyprinaldi

  committed
  48b24f6

Commits on Jun 4, 2024

• [fix] Update ace parser notation

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  anthonyprinaldi

  committed
  7086e40

Commits on Jun 6, 2024

• [fix] Change all references of experiment to treated

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  f028331

Commits on Jun 7, 2024

• [fix] Add log for skipping ACE correlation

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  anthonyprinaldi

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  1792dba

• [fix] Update ace stats parser and docs

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  anthonyprinaldi

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  280d1c1

Commits on Jun 10, 2024

• Merge branch 'dev' into ar-ace_fixes

  anthonyprinaldi

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  762de7c

Commits on Jun 12, 2024

• [wip] Update the ACE docs for the video tutorial

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  ecf4303

• [docs/fix] small syntax fix for duplicated link target name

  jono3030

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  7e0938e

Commits on Jun 14, 2024

• [fix] Update directories for new warping script

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  anthonyprinaldi

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  c890787

• ACE first production version implementation PR #114 from AICONSlab/ar-ace_fixes

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  jono3030

  authored
  567dde3

Commits on Jun 19, 2024

• [fix] Add ACE model directories

  anthonyprinaldi

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  fdade77

• [fix] Add default printing for vox downsample ACE

  anthonyprinaldi

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  4d40ba0

• [feat] improve MIRACL installation script

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  jono3030

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  628fa8e

• [feat/fix] increment MIRACL version and fix build.sh

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  67151f9

Commits on Jun 20, 2024

• [feat] add minor improvements

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  df03320

• [feat] rename build.sh to install.sh

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  696ff1c

• [docs] make several improvements

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  jono3030

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  4ed5e85

Commits on Jun 21, 2024

• [docs] make several improvements

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  jono3030

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  0d188ee

• [docs] replace mentions of build.sh w/ install.sh

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  611fb52

• [fix] Increase description for adding ACE model files

  anthonyprinaldi

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  aa09b59

• [fix] Correct path to MIRACL GUI icon

  anthonyprinaldi

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  84ed8f7

• [fix] Overwrite warp file if it exists

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  anthonyprinaldi

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  99f6d30

• [fix] Group brain patch arg with seg group

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  anthonyprinaldi

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  83a1ca5

• [fix] Remove default side argument ACE

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  anthonyprinaldi

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  e702d68

• [fix] Update ace documentation to match sample data

  anthonyprinaldi

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  d024454

• Merge pull request #127 from AICONSlab/jo-release_prep

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  jono3030

  authored
  3864160

• Merge pull request #126 from AICONSlab/ar/ace-minor-docs

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  anthonyprinaldi

  authored
  ac5e092

• [docs] clear up confusing warning for Win install

  jono3030

  committed
  de269a3

• Merge branch 'dev' into jo-release_prep_docs

  jono3030

  authored
  a57c7dd

• Merge pull request #128 from AICONSlab/jo-release_prep_docs

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  jono3030

  authored
  7b6cd15

Commits on Jun 24, 2024

• [fix] Update ACE docs for single subject flow

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  anthonyprinaldi

  committed
  5abb312

• [docs] Add docker mounting description ACE

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  anthonyprinaldi

  committed
  3ba1b70

Commits on Jun 26, 2024

• [fix] Add full length flags to docs

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  anthonyprinaldi

  committed
  b29222b

Commits on Jun 27, 2024

• [docs] Add smaller batch size for ACE tutorial

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  anthonyprinaldi

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  3337aa2

• [fix] Add container name to successful install

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  anthonyprinaldi

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  ba410cf

• [docs] Add GPU explanation in installation page

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  anthonyprinaldi

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  9d53606

• [docs] Update sample data locations

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  anthonyprinaldi

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  1e0a108

• [feat] add script to download sample data

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  jono3030

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  2f90ada

• [feat] add sample data download script to container /usr/bin

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  jono3030

  committed
  429815d

• [fix] change permissions for download script

  jono3030

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  a96e46c

Commits on Jun 28, 2024

• Merge pull request #131 from AICONSlab/jo-download_sample_data_script

  Show description for 0e0f0fc
  anthonyprinaldi

  authored
  0e0f0fc

• [docs] changed formatting and syntax

  jono3030

  authored
  11c91fa

• [docs] change syntax and add more detail to GPU

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  jono3030

  authored
  222acc9

• Merge pull request #130 from AICONSlab/ar/bugfix-ace-docs

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  jono3030

  authored
  66642bf

• [docs] Update ace docs to use download script

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  anthonyprinaldi

  committed
  9da779a

• [feat] replace shm_size with mem_limit

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  jono3030

  committed
  77ba804

• [docs] add note about download script to data section

  jono3030

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  16a6c48

• Merge pull request #132 from AICONSlab/ar/add-data-download-docs

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  anthonyprinaldi

  authored
  6efe72f

• Merge pull request #133 from AICONSlab/jo-release_prep

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  anthonyprinaldi

  authored
  d603e97

Commits on Jul 3, 2024

• [docs/fix] add code block to ace_flow.rst

  jono3030

  authored
  bc58af0

Commits on Jul 4, 2024

• Merge pull request #137 from AICONSlab/jo-small_doc_fix

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  anthonyprinaldi

  authored
  9c23860

• [fix] Create output folder ace

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  anthonyprinaldi

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  ea7c211

• [docs] Add main output of ace stats

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  anthonyprinaldi

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  af5d9be

• [docs] Add explanation to mounting volumes

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  anthonyprinaldi

  committed
  cedff4a

Commits on Jul 5, 2024

• [docs] Spelling mistake in TOC

  anthonyprinaldi

  committed
  c1249f6

Commits on Jul 9, 2024

• [fix] Add shm back to install script

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  anthonyprinaldi

  committed
  d3b9406

• [docs] Add more description to ace output

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  anthonyprinaldi

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  180eb40

• [docs] Add separate video tutorial section for ACE

  anthonyprinaldi

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  3502194

• [docs] Add registration validation note

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  anthonyprinaldi

  committed
  71487a4

• [feat] change cli help text on shm

  jono3030

  authored
  6feef3b

• Merge pull request #140 from AICONSlab/ar/139-shared-memory-size-in-install-script-docker-compose

  Show description for a7aa6e3
  anthonyprinaldi

  authored
  a7aa6e3

Commits on Jul 11, 2024

• [docs] Add resolutoin for ACE mode 1

  anthonyprinaldi

  committed
  4248fcb

• [feature] Update MIRACL version for ACE

  anthonyprinaldi

  committed
  cc53626

• [fix] Update sylabs token

  anthonyprinaldi

  committed
  8701e33

• [docs] Add youtube playlist link

  anthonyprinaldi

  committed
  6e7711d

• [feat] add first version of ACE flow GUI

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  jono3030

  authored and

  anthonyprinaldi

  committed
  528c20a

• [feat] add script to extract cli parser help text

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  jono3030

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  anthonyprinaldi

  committed
  c19e5ca

• [fix] fix spelling mistake in parser help

  

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  5734e99

• [feat] change main tab name to 'Main'

  

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  1af5382

• [feat] implement label tool tip from parser help

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  jono3030

  authored and

  anthonyprinaldi

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  44f88c0

• [fix] correct default ref for --rca_skip_cor

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  jono3030

  authored and

  anthonyprinaldi

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  db1cf52

• [feat] change utility fn name for text widget

  

  jono3030

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  9a2be5c

• [feat] modularize flag creator

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  jono3030

  authored and

  anthonyprinaldi

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  5bea110

• [feat] add conversion tab structure

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  jono3030

  authored and

  anthonyprinaldi

  committed
  5fb411f

• [docs/fix] add code block to ace_flow.rst

  

  jono3030

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  33955b9

• [fix] fix incorrect syntax for install.sh run instructions

  

  jono3030

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  2c5f3b4

• [fix] improve clarity of arg default syntax

  

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  81cf684

• [feat] created new utility widgets and updated existing instances

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  jono3030

  authored and

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  committed
  c837b34

• [feat] finish conversion tab implementation

  

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  78b9d4b

• [feat] add script docstrings and rename reg and vox/warp tabs

  

  jono3030

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  6769a19

• [fix] fix incorrect verbose flag syntax in ACE parser

  

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  162878e

• [feat] complete vox/warp and add/amend util widgets

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  jono3030

  authored and

  anthonyprinaldi

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  0a10381

• [fix] add missing defaults in help text for parser

  

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  a727c22

• [feat] implement clusterwise tab and modified util widget fn

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  jono3030

  authored and

  anthonyprinaldi

  committed
  f2fa88e

• [fix] add missing default in parser help text

  

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  67ee505

• [fix] correct syntax mistake

  

  jono3030

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  38e014e

• [feat] add correlation/stats tab and amend text field widget

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  jono3030

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  anthonyprinaldi

  committed
  a845e00

• [feat/fix] amend util widget and fix existing invocation

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  jono3030

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  2b2ed24

• [feat] implement heatmap tab

  

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  936672b

• [fix] add workaround for reg module boolean flags

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  jono3030

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  committed
  5b676e2

• [fix] correct in script headers

  

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  6873327

• [feat] change size of GUI and name of app run fn

  

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  9938628

• [feat] add/implement segmentation tab/view

  

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  c8ee104

• [fix] change description text for single vs group in main tab

  

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  583be66

• [feat] change order of parser args to make grouping clearer

  

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  authored and

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  6347539

• [feat] Add ability to call GUI from CLI without any args

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  anthonyprinaldi

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  39d701d

• [feat] Add help message box to ACE GUI

  anthonyprinaldi

  committed
  577737a

• [fix] Add ternary operator to treatment directory arg

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  anthonyprinaldi

  committed
  0be8fe2

• [fix] Allow ACE GUI to print real-time and catch errors

  Show description for 6769dc9
  anthonyprinaldi

  committed
  6769dc9

• [fix] Remove duplicate ACE GUI controller file

  anthonyprinaldi

  committed
  77f18ba

• Merge pull request #141 from AICONSlab/ar/second-round-ace-fixes

  Show description for 2303183
  anthonyprinaldi

  authored
  2303183

• [docs] Fix formatting for bullet points

  anthonyprinaldi

  committed
  2d5bfbc

• Merge pull request #142 from AICONSlab/jo-ace_gui_paper

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  jono3030

  authored
  0314e52

• Merge pull request #143 from AICONSlab/ar/docs-fixes-ace

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  jono3030

  authored
  9f6846a

• [docs] Update ace_flow.rst

  Show description for e9b9532
  anthonyprinaldi

  authored
  e9b9532

• Merge pull request #146 from AICONSlab/ar/sphinx-format-fix

  Show description for 1470c60
  jono3030

  authored
  1470c60

Commits on Jul 12, 2024

• [docs] Fix stale ACE links

  anthonyprinaldi

  committed
  33c375a

• [docs] Update data links to huggingface

  anthonyprinaldi

  committed
  3a22c80

• Merge pull request #147 from AICONSlab/ar/docs-fix-for-stale-ace-links

  Show description for d9cdb15
  jono3030

  authored
  d9cdb15

Commits on Jul 16, 2024

• [fix] Allow heatmap to only work with one group

  anthonyprinaldi

  committed
  2d40718

• [fix] Voxelization bug coming from float32 data type

  Show description for 0ec11cc
  anthonyprinaldi

  committed
  0ec11cc

• [fix] Rename instance segmentation

  anthonyprinaldi

  committed
  f7bb17b

• [feat] Update instance segmentation

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  anthonyprinaldi

  committed
  01b9bc5

• [fix] Add description to instance segmentation

  anthonyprinaldi

  committed
  0ec090e

• [feat] Add script to count neurons and summarize in csv

  anthonyprinaldi

  committed
  de0eef6

Commits on Jul 17, 2024

• [feat] Add instance seg and neuron count to seg CLI

  anthonyprinaldi

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  479cd3c

• [wip] adding ace validate clusters function

  AAttarpour

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  be57795

• [wip] Format validate clusters

  anthonyprinaldi

  committed
  ff82773

Commits on Jul 21, 2024

• [wip] Validate clusters fixes

  anthonyprinaldi

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  fad28da

• [fix] Format and refactor ACE cluster neuron count

  anthonyprinaldi

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  1513f35

• [feat] Add instance seg to ACE workflow

  anthonyprinaldi

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  50de7e3

• [feat] Add validate clusters to ACE workflow

  anthonyprinaldi

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  e7cc7fc

Commits on Jul 25, 2024

• [bugfix] Voxeliztion missing arg

  anthonyprinaldi

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  6a371cc

• Merge pull request #151 from AICONSlab/ar/bugfix-ace-comparison-flow

  Show description for f975b63
  jono3030

  authored
  f975b63

Commits on Aug 11, 2024

• Merge branch 'dev' into ar-ace_fixes_v2

  anthonyprinaldi

  committed
  41ba903

• [fix] Allow None argument for brain side

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  anthonyprinaldi

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  448c6a1

• [fix] Arg name not updated correctly

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  anthonyprinaldi

  committed
  90cb67c

• [fix] Update validate clusters logic in the ace workflow

  anthonyprinaldi

  committed
  656bb36

• [fix] Remove use of redundant variable

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  anthonyprinaldi

  committed
  1bcc7c8

• [fix] Allow zero slice skip to be passed

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  anthonyprinaldi

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  65814b5

• [fix] Switch from using regionprops_table to regionprops

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  anthonyprinaldi

  committed
  f5406e4

• [fix] Fix brain patch percentage arg

  Show description for 6ce680e
  anthonyprinaldi

  committed
  6ce680e

Commits on Aug 12, 2024

• [fix] Remove unused parser args

  anthonyprinaldi

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  6de941f

• [fix] Match parser args to ace stats

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  anthonyprinaldi

  committed
  d0a91e4

Commits on Aug 13, 2024

• [fix] Correct handling of model outputs

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  anthonyprinaldi

  committed
  5576604

• [fix] Refactor validate clusters

  Show description for f511a01
  anthonyprinaldi

  committed
  f511a01

Commits on Aug 14, 2024

• [feat] ace fine tune script and config file

  

  Ahmadreza Attarpour

  committed
  c61dd23

Commits on Aug 15, 2024

• [fix] Udpdate ace stats default values

  anthonyprinaldi

  committed
  370fca4

Commits on Sep 6, 2024

• [format] Organize imports

  anthonyprinaldi

  committed
  622dd86

• [fix] Update parser details and usage

  anthonyprinaldi

  committed
  f1de6e8

• [fix] Handle args better

  anthonyprinaldi

  committed
  91ad5dd

• [fix] Modularize image loading

  anthonyprinaldi

  committed
  11743d8

• [fix] Modularize transforms

  anthonyprinaldi

  committed
  318aedd

• [fix] Modularize dataloaders

  anthonyprinaldi

  committed
  3e43a99

• [fix] Modularize model building

  anthonyprinaldi

  committed
  14d13f9

• [fix] Modularize optimizers

  anthonyprinaldi

  committed
  8668506

• [fix] Modularize train loop

  anthonyprinaldi

  committed
  fd3b27e

• [format] Format entire script

  anthonyprinaldi

  committed
  b72c372

Commits on Oct 8, 2024

• [fix] Remove dynamic unet no longer used

  anthonyprinaldi

  committed
  5f64fe3

• [fix] Correct default model filepath based on docker/sing structure

  anthonyprinaldi

  committed
  127291d

• [fix] Add torchio req for finetune

  anthonyprinaldi

  committed
  6525fe7

• [feat] Add ace_finetune to miracl seg CLI

  anthonyprinaldi

  committed
  69f1f38

• [fix] Remove bug in data transforms

  anthonyprinaldi

  committed
  e0349de

• [fix] Update model_state default to trained

  anthonyprinaldi

  committed
  e66eeac

• [feat] Update default config values and add options

  anthonyprinaldi

  committed
  d011642

• [docs] Add ACE finetune usage to docs

  anthonyprinaldi

  committed
  b73f00e

• [fix] Add new ace features to CLI usage

  anthonyprinaldi

  committed
  e2d8595

• [docs] Add new ace parser flags to docs

  anthonyprinaldi

  committed
  7705c19

• [fix] Spelling mistake

  anthonyprinaldi

  committed
  f2515ca

• [fix] Increase verbosity of parser

  anthonyprinaldi

  committed
  f7785ea

• [docs] Add instance seg documentation

  anthonyprinaldi

  committed
  4a758e9

• [docs] Add neuron_count documentation

  anthonyprinaldi

  committed
  ff144c4

• [docs] Update index for segmentation

  anthonyprinaldi

  committed
  6ab228f

Commits on Oct 11, 2024

• [docs] Update ace workflow output files

  Show description for 83ca5bc
  anthonyprinaldi

  committed
  83ca5bc

Commits on Nov 7, 2024

• [feat/fix] Merge pull request #152 from AICONSlab/ar-ace_fixes_v2

  Show description for 5f1f071
  jono3030

  authored
  5f1f071

Commits on Nov 8, 2024

• Merge branch 'dev' into ar/ace-finetune

  jono3030

  committed
  a769354

• [feat] Merge pull request #153 from AICONSlab/ar/ace-finetune

  Show description for 3ca8443
  jono3030

  authored
  3ca8443

Commits on Dec 5, 2024

• [feat] update .gitignore to ignore Sphinx _build dir

  jono3030

  committed
  4ba0c25

• [docs/fix] correct two minor errors

  jono3030

  committed
  7cc96b1

• [docs] update tested OS list and add warning about sudo use with install.sh

  Show description for f3666ce
  jono3030

  committed
  f3666ce

Commits on Dec 6, 2024

• [feat] start refactoring install.sh to prep for updated functionality

  Show description for 1c37a3b
  jono3030

  committed
  1c37a3b

• [feat] refactor install.sh into functions

  jono3030

  committed
  111299f

• [feat] added a fn to check if install.sh is run using sudo

  jono3030

  committed
  019b727

• [feat] add interactive prompt to install.sh

  Show description for b90d68a
  jono3030

  committed
  b90d68a

• [feat] add random name generator fn

  Show description for d3534ac
  jono3030

  committed
  d3534ac

• [fix] remove duplicates from surname list

  jono3030

  committed
  037dbdf

Commits on Dec 12, 2024

• [docs] make installation instructions more verbose

  jono3030

  committed
  d163173

Commits on Dec 13, 2024

• [docs/feat] exclude prompts from copybutton

  Show description for daf9b64
  jono3030

  committed
  daf9b64

• [feat/fix] add interactive data location prompt and bugfixes

  Show description for 5f0dc8c
  jono3030

  committed
  5f0dc8c

Commits on Dec 14, 2024

• [fix] uncomment echo cmds used for testing

  jono3030

  committed
  fab2c3c

Commits on Dec 16, 2024

• [docs] add content to installation section

  Show description for e131b68
  jono3030

  committed
  e131b68

• [feat] minor Bash improvements and validations

  jono3030

  committed
  cba95e6

• [fix] pin typer version to 0.11.1

  Show description for 800a33c
  jono3030

  committed
  800a33c

• [feat] add size of datasets to help menu

  jono3030

  committed
  d219128

• Merge pull request #154 from AICONSlab/jo-typer_fix

  Show description for b370c15
  jono3030

  authored
  b370c15

• Merge pull request #156 from AICONSlab/jo-sphinx_dev

  Show description for fa13c14
  jono3030

  authored
  fa13c14

• Merge pull request #155 from AICONSlab/jo-andrew_feedback

  Show description for 850b17c
  jono3030

  authored
  850b17c