Connectometry analysis
use –action=
cntto 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. To test the longitudinal change, specify –foi=longitudinal |
Parameters
| Parameters | Default | Description |
|---|---|---|
| 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_iteration | 16 |
assign the number of pruning applied to remove noisy results. |
| 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) |