Add DTI measures - #41

Draft

valosekj wants to merge 59 commits into

mainfrom

jv/17-add_dti_measures

Commits on Apr 8, 2026

Add initial version of script to process DWI data
valosekj
committed
8a976d1
Add configurable preprocessing flags to test different processing steps from https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/issues/17#issuecomment-4135884173
valosekj
committed
89f5e15
Add config file for DWI processing
valosekj
committed
f1abfe4
Log preprocessing arguments to file
valosekj
committed
0580670
Define log prefix to have consistent log files for T2w and DWI files
valosekj
committed
57fa1bf
Process DTI metrics in parallel for faster processing
valosekj
committed
99501cc

Commits on Apr 14, 2026

use include_list to include all spine-generic HC
valosekj
committed
eff943f
Add script to generate PAM50 DTI figures
valosekj
committed
85e9922

Commits on Apr 15, 2026

Refactor DTI lineplot creation to share y-axis limits and improve subplot layout
valosekj
committed
1ad4253

Commits on Apr 21, 2026

use x-axis label and tick numbers only on bottom row
valosekj
committed
49768f6
remove unnecessary note about warp field
valosekj
committed
ac9dba9
improve comments
valosekj
committed
ea6447a
move DTI computation before template reg for easier code readability
valosekj
committed
1e71aa9
Shorten the DWI section by consolidating commands; improve commnets
valosekj
committed
398ce20
Add per-sex plotting
valosekj
committed
38adbe5

Commits on Apr 24, 2026

clarify PAM50 template to DWI space comments
valosekj
committed
b000f86

Commits on Apr 27, 2026

Commits on Apr 29, 2026

Commits on May 5, 2026

use CC instead of MI for dmri moco
valosekj
committed
97d8c8c

Commits on May 12, 2026

Add vertebral level range restriction and improve data filtering in DTI figure
valosekj
committed
973fbec

Commits on May 15, 2026

Use only 2 labels for T2w -> PAM50 registration to be consistent with SCT course.
valosekj
committed
0d0b607

Commits on May 19, 2026

Commits on May 20, 2026

Commits on May 23, 2026

make the script compatible with DTI metrics based on eigenvalues
valosekj
committed
da635fb
tweak font size
valosekj
committed
e6b1730

Commits on Jun 3, 2026

move the vertical lines to be exactly between
valosekj
committed
30892ae
Add script to compare FA between warp and interp methods in PAM50 space for a single subject
valosekj
committed
af6d1fb
Rename DTI scripts
valosekj
committed
ce66375
Cleanup eigenvalue related code.
valosekj
committed
8ca5aff
Organize the two DWI PAM50 methods (warp, interp) into sections to improve code readability
valosekj
committed
b6c30d0
improve comments
valosekj
committed
94f0996
Unify DTI metric extraction loops (warp to PAM50, interpolate to PAM50, native)
valosekj
committed
6e4d34d
improve comments
valosekj
committed
c446583
use sct_deepseg spinalcord for both T2w and DWI
valosekj
committed
92c865e
remove preprocessing flags
valosekj
committed
bcdfa5a
minor description update
valosekj
committed
750c3c7
update label_if_does_not_exist to use TTS
valosekj
committed
0542416
update requirements and authors
valosekj
committed
85a8c26

Commits on Aug 11, 2026

make explicit that the extra block of code is done perslice
valosekj
committed
bada739
add an extra section to extract perlevel matrics in the native space
valosekj
committed
181f8df
comment out WM and uncomment DC, CST, and spinal lemniscus
valosekj
committed
81fc3db
remove script_args
valosekj
committed
f48af89
update path_output
valosekj
committed
f94f47e
comment out PAM50 and perslice native extraction
valosekj
committed
73c441b
clarify file_out for perslice native metrics
valosekj
committed
1600ba0
clarify file_out for perlevel native metrics --> aggregate metrics across subjects to a single CSV per metrics
valosekj
committed
ba8c603

Commits on Aug 12, 2026

Revert SUBJECT back to file_out to prevent CSV file overwriting
valosekj
committed
335b9a3

Commits on Aug 22, 2026

- uncomment PAM50 interpolation to test https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/5236
valosekj
committed
99375ee