Connectometry Analysis
Use
--action=cnt
to initiate [Step C3 Connectometry].
Examples
1. Use a multiple regression model with three variables (0:SEX, 1:BMI, 2:AGE) to study how BMI (the second variable) affects the brain connection in the CMU 60 connectometry database.
dsi_studio --action=cnt --source=CMU60.db.fib.gz --demo=CMU60.txt --variable_list=0,1,2 --voi=1 --roi=FreeSurferDKT:left_precentral --output=CMU60
2. Use ROI and ROA to limit connectometry analysis on subjects with specific demographics: scanner=1 and group not equal to 3.
dsi_studio --action=cnt --source=study.db.fib.gz --demo=demo.csv --roi=ROI.nii.gz --roa=ROA.nii.gz --select="scanner=1,group/3" --variable_list=2,4,5 --voi=5
3. Windows batch script to test each variable from 5 to 37, with variables 2 and 3 included as covariates.
for /l %%G in (5,1,37) do (
dsi_studio --action=cnt --source=connectometry.sdf.db.fib.gz --demo=PANSS.csv --variable_list=2,3,%%G --voi=%%G > log%%G.txt
)
Core Functions
Parameter | Description |
---|---|
source |
Specify the db.fib.gz file. |
demo |
Assign the path to the demographic CSV or text file. |
variable_list |
Assign the study variables for regression. Use commas to include multiple variables. Example: --variable_list=0,1,2 includes the first three variables. |
voi |
Specify the “variable of interest” for multiple regression. Use --voi=0 for the first variable, --voi=1 for the second, etc. For longitudinal analysis, use --voi=longitudinal . |
Parameters
Parameter | Default | Description |
---|---|---|
t_threshold |
2.5 |
Assign the t-threshold for correlational tracking. |
length_threshold |
20 voxel distance |
Specify the minimum tracking length for correlations. |
fdr_threshold |
0 |
Set a nonzero FDR threshold (e.g., 0.05) to enable FDR control. |
permutation |
2000 |
Specify the number of permutations used in analysis. |
thread_count |
Hardware max | Define the number of threads for computation. |
tip_iteration |
16 |
Number of pruning iterations to reduce noise. |
exclude_cb |
1 |
Use --exclude_cb=1 to exclude the cerebellum from analysis. |
no_tractogram |
1 |
Set to 1 to avoid generating 3D tractogram images (output files are still generated). |
output |
Demographics path | Specify the prefix for all output files. Defaults to the demographics file name with the study variable appended. |
Optional Functions
Parameter | Description |
---|---|
select |
Select subjects for analysis. Example: --select=Gender=1,Age>20 filters subjects with Gender=1 and Age > 20. |
seed, roi, roa... |
Define regions to limit the tracking areas (see --action=trk for details). |
Updates Based on Code Features
Features Found in Source Code:
- Multiple Regression: The class
group_connectometry_analysis
handles the regression model and adjusts QA values based on statistical models. - FDR Analysis: The function
calculate_FDR
computes the false discovery rate to identify significant findings. - Exclusion of Cerebellum: The method
exclude_cerebellum
removes cerebellum-related data whenexclude_cb=1
. - SPM Generation: Statistical Parametric Mapping is computed via
calculate_spm
and results are saved usingsave_result
. - Report Generation: The
generate_report
method creates a detailed HTML visualization of findings.