Single workflow - #5

Draft

arkiev wants to merge 113 commits into

mainfrom

single_workflow

Commits on Mar 17, 2026

ported over files from personal repo to shared repo
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cb38ded

Commits on Mar 18, 2026

working pipeline but DWI is python
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2155d6e

Commits on Mar 19, 2026

test that is running
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7f4fcb1
fixed DWI T1 coregistration and reintroduced it to -rpe_none, updated scatter, updated checkpoints, didn't crash
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fa62a9e
fixes to github error 67834536377
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5b3437b

Commits on Mar 20, 2026

Commits on Mar 23, 2026

updated docs to reflect integration of single-workflow changes
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108ca6e

Commits on Mar 24, 2026

removed unneeded import
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ece2e00

Commits on Mar 26, 2026

Commits on Mar 27, 2026

suppressed registration check for not SPIRIT, runs to compeletion - CHECK TEMPLATE T1!
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b8d9f5a

Commits on Mar 30, 2026

removed registration check for non-spirit phantoms
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25b5f91

Commits on Mar 31, 2026

removed reg check and rotations - seems redundant given scan protocol
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c0fee27

Commits on Apr 1, 2026

removed fallback to SPIRIT if failed for 120E
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721de55
reverted back to original jsons
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58206e5
pydrafied phantom_processsor file
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2d83ff3
pydrafied version that seems to work
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66f5c64
updated flowchart
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33a31ab
updated flowchart code again
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0a8ff69
added in temperature calibration plotter
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723d664
plot mode and estimate mode enabled
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7b1015a

Commits on Apr 2, 2026

removed redundant rotations.txt. added functionality to handle adc_mean.csv and vial LUT
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44be0c5
zoom feature and toggle vials
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ecd1212
integrated vial temp estimates
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6c1f558

Commits on Apr 17, 2026

tidy up
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cab8e7c
add compare-plots command for cross-session measurement comparison

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e4b8e15
embed phantom name in T1/T2 mapping HTML; improve compare-plots phantom detection

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claude
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8e939ad
improve compare-plots labels, font sizes, and marker sizes

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edde29e
updated 120E template data
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122db18
removed registration check and rotations (redundant with scanning setup protocol)
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4d3bb3a
120E pipeline test works
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28803fb

Commits on Apr 20, 2026

input type agnostic and added in 120E relaxometry compatibility
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b009721
replacing "vials_labelled" with VialsLabelled
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7c86110

Commits on Apr 22, 2026

misc plotting updates
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c15e709
added missing -interp nearest and created dockerfile
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e9196d1
update docker to cater beyond macs
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00c65d2
docker build fixes
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e85967d
nifti, mif and zipped variants added to possible inputs
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c918890

Commits on Apr 23, 2026

temp calibration inclusion in main workflow
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93562be
reorder docker readme
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80a74b2

Commits on Apr 29, 2026

Commits on Apr 30, 2026

updated median absolute deviation calculation to use median (not mean) in outer bracket
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e32c733

Commits on May 4, 2026

updating parsing to handle SEQ#
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b5c9f33

Commits on May 5, 2026

now handles filenames with no separator (eg: TE50)
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b368c61
misc superficial updates
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6fab8e0

Commits on May 6, 2026

added in noise segmentations for CNR and SNR
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ba7da58

Commits on May 12, 2026

added DWI SNR CNR and updated template image/vials
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2c2c5ff

Commits on May 13, 2026

fixed cleanup bug and added in show/hide all vials toggle
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b19a091
added in SNR and CNR for T1 and T2 contrasts
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38431da

Commits on May 15, 2026

included cpu_thread definition for ants reg
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1888575

Commits on May 20, 2026

Commits on May 21, 2026

SNRalternate working
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fde7043
addressing github error messages
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9865eb3

Commits on May 22, 2026

Commits on May 25, 2026

rewriting package in terms of pure pydra workflows
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78973b3

Commits on Jun 9, 2026

testing out utility of Phantomkit for PET
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0fdebf8
updated template vial E, colormap and tidy up
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569522e
abandoning colourmap changes
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72ddbe7
using mrstats for data extraction
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f87dbd3

Commits on Jun 10, 2026

image viewer tweaks
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c74fcb0

Commits on Jun 12, 2026

misc changes to comply with recent pydra update
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d6aa775
remove second workflow file
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4bc22c5

Commits on Jun 13, 2026

Commits on Jun 14, 2026

updating output names to reflect processing
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9959a2b

Commits on Jun 15, 2026

made dwigradcheck a processing option, --nocleanup now keeps other tmp files
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0e0dbff

Commits on Jun 16, 2026

updated workflow to reflect recent changes
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276a7af

Commits on Jun 17, 2026

uploading docker files
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0118ad4
integrated longitudinal comparator
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a0f729c
merge longitudinal plot command from LongWorkflow
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d41ee51

Commits on Jun 22, 2026

Longitudinal: ADC per vial (all vials)
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e0d1fb3
Merge branch 'LongWorkflow' into single_workflow
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835efc7

Commits on Jul 14, 2026

working model
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189f8f1
updated to match filename convention
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0d0c231
T1_mapping fix
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f1eee03

Commits on Jul 15, 2026

t1 SNR/CNR bugfix
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c99ec2a
eddy nthr functionality
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12e9d75
Merge name_convention_test into single_workflow

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claude
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b4131e3

Commits on Jul 16, 2026

Working GUI
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e0d712a
updated for gui functionality use in docker - needs testing
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038e2af

Commits on Aug 2, 2026

toggle all on/off long and comp
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7bc9088

Commits on Aug 9, 2026

docker gui test build test
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d36c97f
Revert "docker gui test build test"
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df3605f

Commits on Aug 10, 2026

Reapply "docker gui test build test"
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097201b
viewer error fix
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5110bd4
Force unbuffered stdout on pipeline/plot subprocesses in the GUI

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8526f71
Always pull and restart fresh in the GUI launcher script

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af29e00
Fix silent hang when GUI output path isn't actually mounted

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2c6038f

Commits on Aug 11, 2026

Restore native-contrast QC outputs to their own subfolder

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9a11ea6
Merge Longitudinal tab into Compare with a toggle checkbox

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3b6d041

Commits on Aug 12, 2026

Fix Stage 1 crash on MIF-format anatomical series, surface real errors

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a483d2c

Commits on Aug 13, 2026

Fix TE/TI value extraction picking up trailing scan reference number

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64c49b2
Auto-handle foreign/flat DICOM dumps via dcm2niix fallback

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40a0f4d
Warn when a folder name's TE/TI/AP-PA disagrees with its image header

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f45dc0d

Commits on Aug 17, 2026

Add vendor comparison feature: validate ADC/T1/T2 against vendor maps

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e234db1
Fix vendor-compare viewer hang, scope vials, restore reference series

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706c917
Fix vendor-compare viewer hang for non-MIF images, ADC unit scaling, error bars
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f263e84

Commits on Aug 19, 2026

Add per-dataset show/hide toggle buttons to vendor-compare chart
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02d4391
Hide error bars when their dataset is toggled off
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0466061