Merge Dev to main - #5

Merged

ironictoo merged 156 commits into

mainfrom

Mar 3, 2026

Commits on Oct 13, 2022

Update DCE.yml
lsaca05
authored
15f646a

Commits on Oct 19, 2022

use MPRAGE images to generate matter masks (#3)
lsaca05
authored
6c3cfbd

Commits on Oct 20, 2022

force zip masked VFAs, exlude jsons from rm
lsaca05
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d4a977d
name changes (t1w -> T1)
lsaca05
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5446d74

Commits on Oct 21, 2022

add site name to report title
lsaca05
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b2de7e5

Commits on Oct 26, 2022

added a sort function to get data in BIDS compliant structure
ironictoo
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d477b51
added missing task name to rest
ironictoo
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29c05dc

Commits on Oct 27, 2022

Merge branch 'run-all-script' into freesurfer
lsaca05
committed
bacc5c7

Commits on Nov 15, 2022

Use ANTS for registration, displacement/corrcoef graphs, some renaming, add institution name to report, registration QC WIP
lsaca05
committed
5aedc05

Commits on Nov 23, 2022

change disp graph colors, mix ANTs with Freesurfer, re-register (prototype) based on zeros
lsaca05
committed
399b053
Update DCE.yml
lsaca05
authored
aa5d1af

Commits on Nov 29, 2022

gm reg QC, reiterate reg based on weighted average zeros, disp params more specific, freesurfer option
lsaca05
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ae6d490

Commits on Nov 30, 2022

added log files, bit of cleanup
lsaca05
committed
79caf2a

Commits on Dec 8, 2022

add basic logging and primitive progress bar
lsaca05
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0b3c1a2

Commits on Dec 9, 2022

BIDS script tailored towards GRASP DICOMs
lsaca05
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faa3097
remove fail fast option, force it now
lsaca05
committed
897462b
condense rm chains with a bit of regex
lsaca05
committed
d82eb3c

Commits on Dec 12, 2022

WIP: ETA scaling adjustments (3min@end)
lsaca05
committed
8b8527f

Commits on Dec 13, 2022

TemporalResolution calculated + added to config.json as part of BIDS script
lsaca05
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5caa8eb

Commits on Dec 14, 2022

start tailoring BIDS script toward our data, add aif mean script
lsaca05
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85c11e1

Commits on Dec 15, 2022

refactoring
lsaca05
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506dc67
rename a variable
lsaca05
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4c8f645
refactoring, larger time scale factor if no GPUFIT detected
lsaca05
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c142047
Merge branch 'progbar' into dev
lsaca05
committed
a609a46
force ff in DCE script, update DCE.yml
lsaca05
committed
8f49266

Commits on Jan 6, 2023

long have we waited, AFNI dependency eliminated
lsaca05
committed
0132eb5
Update DCE.yml
lsaca05
authored
42c583e

Commits on Jan 11, 2023

increased time estimation factor
lsaca05
committed
727bfaa
Merge branch 'main' into dev
lsaca05
committed
a76fb8f
Update DCE.yml
lsaca05
authored
5d5150e
Update DCE.yml
lsaca05
authored
dc78d95

Commits on Jan 12, 2023

clean up old dce_all opts, fix GPUFIT_PATH + add to T1 cmd
lsaca05
committed
55b2182

Commits on Jan 26, 2023

update reqs and runtime, add dockerfile (WIP)
lsaca05
committed
cdaab33

Commits on Jan 31, 2023

fix GPU detection condition, fix missing endquot in T1 mapping matlab call
lsaca05
committed
d90fc60

Commits on Feb 6, 2023

trim down docker image size to 7-8 gigs
lsaca05
committed
b821f3a

Commits on Feb 9, 2023

Commits on Feb 11, 2023

resolve freesurfer license + hd-bet param pre-load issues
lsaca05
committed
39d47c5

Commits on Mar 2, 2023

complete dockerfile, some fixes for docker compatibility, add docker run script
lsaca05
committed
e1ee4cd

Commits on Mar 8, 2023

Commits on Mar 13, 2023

fix DCE action run cmd, update tag name
lsaca05
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d1aee68
merge docker workflow into DCE workflow, just build lol
lsaca05
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b0077db

Commits on Mar 14, 2023

docker build for MATLAB releases R2020a-R2022b
lsaca05
committed
bc87cb6

Commits on Mar 15, 2023

Commits on Mar 31, 2023

cd out 1 folder further if error
lsaca05
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71a2d84

Commits on May 30, 2023

checkout action in pipeline, since the runner's version of this repo wasn't updating
lsaca05
committed
7a4934c

Commits on Jul 21, 2023

HTML QC report + Double Gaussian Fit Normalization + No correction run fix (#4)
lsaca05
authored
424e8d6

Commits on Jul 26, 2023

Commits on Jul 28, 2023

dims and voxel_size now exist outside of reorient loop, fix commit exception syntax
lsaca05
committed
02c23ed
fix get git commit alt cmd
lsaca05
committed
0672304

Commits on Jul 31, 2023

fix alt get git commit cmd (check_output, __file__)
lsaca05
committed
4cfc87f
check if DCE and AIF have same dims for plot
lsaca05
committed
2ff6b00

Commits on Oct 20, 2023

Commits on Oct 27, 2023

Commits on Oct 30, 2023

back to ROCKETSHIP-dev in github actions yml
lsaca05
committed
9e1c4e1

Commits on Nov 2, 2023

Commits on Nov 16, 2023

Commits on Nov 17, 2023

try newer nvidida/cuda image w/ cudnn8, wipe out fraudsurfer from docker image
lsaca05
committed
1a5b9b2

Commits on Nov 23, 2023

Commits on Dec 1, 2023

t1w to MNI with ANTS instead of FLIRT, fix making list of outliers
lsaca05
committed
65c2576

Commits on Jan 23, 2024

improved log file and figure organization, rename auto_analysis to ktrans_analysis, bit of cleanup, parallelize split into repetitions
lsaca05
committed
773f4e0

Commits on Feb 21, 2024

update README to reflect updated registration and AutoAIF
lsaca05
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29dd33f
forgor wm segmentation in README preprocessing step summary
lsaca05
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d149fdf
update README DCE inputs/outputs
lsaca05
committed
d8c831c

Commits on Feb 23, 2024

add freesurfer wm parc option, many misc fixes, add wmparc subregions to pop report, aggregate AIF curves, log ROCKETSHIP params to pop report, generate excel sheet at end of DCE_all
lsaca05
committed
8e11d14

Commits on Feb 26, 2024

model weight path to repo
lsaca05
committed
2fe7331
oop wrong model weight path, fixed
lsaca05
committed
7331675

Commits on Mar 19, 2024

add proper config.json for dcm2bids purposes
lsaca05
committed
245e4e8

Commits on Apr 19, 2024

Commits on Apr 22, 2024

Update DCE.yml
lsaca05
authored
9948b80

Commits on Apr 26, 2024

pull some spreadsheet values from log files instead of jsons, misc fixes
lsaca05
committed
a53f6f0

Commits on Apr 30, 2024

update DCE.yml action versions
lsaca05
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77f9261
fraudsurfer returns to docker, update ROCKETSHIP func names and args
lsaca05
committed
bc79252
fix cat target filename in DCE.yml, remove unused imports, update requirements.txt
lsaca05
committed
9c5447b
forgor to specify log folder dirs in output logs step
lsaca05
committed
39983b9
update other paths of runner steps
lsaca05
committed
32367cf
fix runner step paths again
lsaca05
committed
591e619
missed one path
lsaca05
committed
a23d1e7
oops i did it again
lsaca05
committed
90092f6
fix docker tag name
lsaca05
committed
ebef15b

Commits on May 18, 2024

split successful cases into include and exclude in spreadsheet and EZQC, add posterior cingulate cortex and medial temporal cortex, alternate aseg thalamus name fix, more accurate recon-all stats r…
lsaca05
committed
ce64783

Commits on May 28, 2024

truncated 1 char too much from wm/gm median
lsaca05
committed
f2647c1

Commits on Jun 5, 2024

skip to DCE if new variant (inherit inputs from base variant), fix matlab DCE cmd, re-add pipeline variant support (comparison mode), account for varying B log name, make population average AIF and…
lsaca05
committed
6a56df0

Commits on Jun 7, 2024

fix case/ktrans report args in DCE_all, recognize when imported AIF in log read, DCE_TR s->ms label
lsaca05
committed
289592c

Commits on Jun 14, 2024

DCEref img plot fix for cases with different coords + use 95th %tile for vmax, fix hematocrit pattern, read AIF status from preprocess cmd, separate excluded cases, add AIF curves graph to pop repo…
lsaca05
committed
b70e8de

Commits on Jun 21, 2024

add threading + more checks + r squared to pop report
lsaca05
committed
95a4df7

Commits on Jun 25, 2024

misc fixes and renames, case report support for no -f (freesurfer) flag, fix failed cases not filling fail dict, fix placement histograms
lsaca05
committed
dfd68b9

Commits on Jul 2, 2024

dynamically list FAs in report, fix EZQC imgs list, init log command var
lsaca05
committed
d2a0edc

Commits on Jul 3, 2024

idk why i moved these mkdirs
lsaca05
committed
138e68d
now I remember
lsaca05
committed
9f5e346
fix dynamic listing of FAs in caes report
lsaca05
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9d30a12
check if source spreadsheet exists before pulling from it
lsaca05
committed
6e873d7

Commits on Jul 11, 2024

new iNESMA filter, paper implementation, not tested
lsaca05
committed
7529b8d
increase array size for similarity/indices arrays
lsaca05
committed
96cfeff

Commits on Oct 30, 2024

refactor: update AIF quality metrics and fix link formatting in pop report
lsaca05
committed
d26dbf9

Commits on Nov 5, 2024

moved aifitness calc to seperate file
ironictoo
committed
ab76bec
rescale AIFitness based on new test splits stats
lsaca05
committed
bc8f64d

Commits on Nov 6, 2024

rename DCE.yml target subject
lsaca05
authored
5360ad8
revert previous commit
lsaca05
committed
bc6daec

Commits on Nov 13, 2024

Commits on Nov 15, 2024

rescale AIFitness tail metric, use mean baseline in base_to_mean metric
lsaca05
committed
daf139c

Commits on Dec 19, 2024

update DCE processing scripts: add smoothing and target args, add checks for file existence, improve Gaussian fitting logic, and enhance normalization calculations
lsaca05
committed
e42bef0

Commits on Dec 21, 2024

Commits on Jan 2, 2025

remove unused scripts: delete obsolete AFNI registration and comparison scripts to clean up the repository, make excel sheet path relative
lsaca05
committed
6c022ea

Commits on Jan 8, 2025

update scripts: add __pycache__ to .gitignore, improve DCE processing logic, and enhance log file handling in case_report.py
lsaca05
committed
1913860

Commits on Jan 15, 2025

Commits on Jan 23, 2025

fix exception memory leak, fix entry move to exclude dict
lsaca05
committed
35d7bc8

Commits on Feb 18, 2025

Commits on Feb 19, 2025

Commits on Feb 20, 2025

idk why i commented out docker push step
lsaca05
committed
33b54dc

Commits on Feb 24, 2025

refactor scripts to improve MATLAB path retrieval, update option flags for preprocessing, add cortical thickness stats to spreadsheet
lsaca05
committed
9b978cb

Commits on Feb 25, 2025

now I remember, because I need secrets for personal account but can only do organizational secrets
lsaca05
committed
7f5d708

Commits on Mar 5, 2025

skip hd-bet if T2w structural image (assuming mouse for now)
lsaca05
committed
e5baf21

Commits on May 21, 2025

Commits on May 23, 2025

attempt to implement locking for distributed processing
lsaca05
committed
e906b72

Commits on Jul 2, 2025

Improves population reporting and concurrency controls
lsaca05
committed
d663ee2

Commits on Jul 3, 2025

feat: add ROCKETSHIP commit hash retrieval and display in reports
lsaca05
committed
02967d8

Commits on Jul 21, 2025

update docker freesurfer version 7.3.2->7.4.1
lsaca05
committed
6bbfe60

Commits on Oct 8, 2025

Commits on Oct 9, 2025

Commits on Oct 11, 2025

move matlab docker portion below most package installations for caching purposes
lsaca05
committed
01f26de

Commits on Oct 15, 2025

re-add freesurfer dependencies for some reason, make deb frontend non-interactive, restore var from other branch that was needed
lsaca05
committed
6231719

Commits on Dec 3, 2025

Commits on Feb 11, 2026

Readme updates
ironictoo
committed
047cfb6
Citation tweak
ironictoo
committed
4b9d168

Commits on Mar 3, 2026

Merge branch 'main' into dev
ironictoo
authored
4259a79