Connectometry analysis

use –action=cnt to initiate [Step C3 Connectometry]

Examples

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

*Use ROI and ROA to limit connectometry analysis on subjects with demographics of 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

*Windows batch for testing each of the variable from 5 to 37, with variable 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

Parameters 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 to be included in the regression model. use comma to include multiple variables.
For example, use –variable_list=0,1,2 to include the first, second, and third variable.
voi specify variable of interest (used only in multiple regression).
–foi=0 will analyze the “first” variable listed in the demographic file,
–foi=1 will analyze the second one.

Parameters

Parameters Default Description
nonparametric 1 specify whether to use nonparametric correlation. The default is on.
t_threshold 2.5 assign the t threshold for correlational tracking.
length_threshold 20 voxel distance assign the length threshold for correlational tracking.
fdr_threshold 0 assign a nonzero FDR threshold (e.g. 0.05) to enable FDR control.
permutation 2000 assign the number of permutation used in the connectometry analysis.
thread_count hardware max assign the number of threads used in the computation.
tip 4 assign the number of pruning applied to remove noisy results.
normalize_qa 1 if qa is used
0 otherwise
specify whether to normalize QA. For metrics other than QA, do not enable normalization.
exclude_cb 1 assign –exclude_cb=1 to exclude cerebellum.
no_tractogram 1 specify 1 to signal DSI Studio NOT to output 3D tractogram pictures. The analysis will still output tractography files, which can be used later to generate tractogram separately.
output path to the demographics file name the file prefix for output all analysis results. The default will be the path to demographics file adding the name of the studying variable.

Optional Functions

Parameters Description
select select subjects for analysis.
For example, –selection=Gender=1,Age>20 select subjects with Gender field equal to 1 and Age older than 20 in the demographics.
seed, roi, roi2, roa… assign regions to limit the tracking region. (see –action=trk for details)