Region and Tract Functions
use –action=
ana
to initiate region or tract functions in [Step T3 Fiber Tracking]
The ana
action can use any post-tracking functions listed under “–action=trk”, including delete_repeat
,output
, export
, end_point
, ref
, connectivity
, connectivity_type
, connectivity_value
, and ROI related commands, such as roi
, roi2
, …etc. Please check out --action=trk
for details.
Examples of Tract Functions:
Convert trk file to txt file
dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz--output=Tracts1.txt
Read track trk file, filter it by ROIs, and output as another trk file
dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts.tt.gz --roi=roi.nii.gz --roi2=roi2.nii.gz --output=filtered_track.tt.gz
Convert trk file to ROI file
dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz --output=ROI.nii.gz
Generate tract density imaging from a trk file.
dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz --export=tdi
Get track statistics from a track file
dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --export=stat
Get track DKI and ODI statistics from a track file
dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --other_slices=DKI.nii.gz,ODI.nii.gz --export=stat
Calculate the connectivity using the tractography and ROI files
dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --connectivity=FreeSurferDKT,my_roi.nii.gz,another_roi.nii.gz --connectivity_value=qa,count,ncount --connectivity_type=pass,end
Examples of Region Functions:
Get the statistics of multiple native-space ROIs
dsi_studio --action=ana --source=my.fib.gz --regions=native_space_roi.nii.gz
Get the statistics of multiple MNI-space ROIs
dsi_studio --action=ana --source=my.fib.gz --regions=mni_space_roi.nii.gz
Get statistics from Freesurfer segmented ROIs using subjects T1W to guide the registration
dsi_studio --action=ana --source=my.fib.gz --regions=aparc+aseg.nii.gz --t1t2=subject_t1w.nii.gz
Get statistics from ROIs of the atlas included in the DSI Studio package
dsi_studio --action=ana --source=*.fib.gz --regions=HCP842_tractography:Cingulum_L,HCP842_tractography:Cingulum_R,HCP842_tractography:Corpus_Callosum
Get the statistics from multiple ROIs of an atlas
dsi_studio --action=ana --source=my.fib.gz --atlas=FreeSurferDKT
Core Functions
Parameters | Description |
---|---|
source | specify the fib.gz file |
Tract Functions
Parameters | Description |
---|---|
tract | Specify the tract file |
output | Use”–output=Tract.txt” to convert the trk file to another format or ROI (assigned output file as NIFTI file) |
export | Export additional information related to the fiber tracts |
Export tract density images
- Use
--export=tdi
to generate a track density image in the diffusion space. To output in x2, x3, x4 resolution, usetdi2
,tdi3
,tdi4
(also applied to the following commands). - Use
--export=tdi_color
to generate a track color density image. - Use
--export=tdi_end
to output only the endpoint.
Export tract profile
- Use
--export=stat
to export tract statistics like along tract mean fa, adc, or morphology index such as volume, length, … etc. - Use
--export=report:dti_fa:0:1
to export the tract reports on “fa” values with a profile style at x-direction “0” and a bandwidth of “1”
The profile style can be the following:
0
: x-direction1
: y-direction2
: z-direction3
: along tracts4
: mean of each tract
You can export multiple outputs separated by “,”. For example,
--export=stat,tdi,tdi2
exports track statistics, tract density images (TDI), subvoxel TDI, along tract qa values, and along tract gfa values.
Region Functions
**Do not specify --tract
if you want to use the region analysis function **
Parameters | Description |
---|---|
region or regions | specify the NIFTI file of a single ROI (–region) or multiple ROIs (–regions) to export region statistics. If the regions are in the MNI space, add “mni” to the file name (e.g. mni_regions.nii.gz) |
t1t2 | if the region is derived from a T1W, then specify the t1w image using –t1t2=t1w.nii.gz for registration with the DWI. |
atlas | Specify the built-in atlas name for export region statistics |
Multiple files can be specified using “+” as the separator. The format can be a txt file or nifti file or from the atlas regions (e.g. –region=FreeSurferDKT:right_precentral+FreeSurferDKT:left_precentral)
The loaded regions can be modified using “smoothing”, “erosion”, “dilation”, “defragment”, “negate”, “flipx”, “flipy”, “flipz”, “shiftx” (shift the roi by 1 in x direction), “shiftnx” (shift the roi by -1 in x direction), “shifty”, “shiftny”, “shiftz”, “shiftnz”.
For example, –region=region.nii.gz,dilate,smoothing –regions=multiple_regions.nii.gz,flipx