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: