Visualization

use –action=vis to initiate 3D rendering interface for visualization

Examples

Load all fib file and its correponding tract file. Add an isosurface,and save the rendering image in horizontal layout.

dsi_studio --action=vis --source=sub001.fib.gz --tract=sub001.tt.gz --cmd="set_zoom,1.0+restore_rendering+add_surface,Full+save_h3view_image,sub001.png"

Load an fib file and a tract file. Set the view from the top and save the rendering image as 1.jpg.

dsi_studio --action=vis --source=test.fib.gz --tract=whole_brain.tt.gz --cmd="set_view,2+save_image,1.jpg,1024 800"

Load an FIB file and keep GUI open:

dsi_studio --action=vis --source=test.fib.gz --stay_open=1

Load multiple TRK files and keep GUI open:

dsi_studio --action=vis --source=test.fib.gz --tract="TRACK1.tt.gz,TRACK2.tt.gz" --cmd=" " --stay_open=1

Load trk and fib files to rendering their 3D images (Windows batch script)

path=C:\Users\frank\Documents\GitHub\DSI-Studio-WIN64\dsi_studio_64
FOR /F "delims=" %%A in ('dir *.fib.gz /b /on') do (
    call dsi_studio.exe --action=vis --source=%%A --tract=%%A.tt.gz --cmd="add_surface,0,0+slice_off+save_h3view_image,%%A.jpg+save_h3view_image,%%A.jpg" > %%A_.txt
)

Core Functions

Parameters	Default	Description
source		specify the fib.gz file for automatic bundle tracking.
stay_open	0	assign “–stay_open=1” to allow GUI to stay open after the command line
tract		(optional) specify the track files to open. To load multiple files, use “,” to separate multiple track files.
cmd		specify the function to execute. Multiple commands can be combined using “+” as the separator (e.g. –cmd=”add_surface+save_image”)

The following commands are for controlling the interface:

• add_surface: add an full brain isosurface (e.g. add_surface,Full). To add partial brain isosurface, replace Full by Left,Right,Upper,Lower,Posterior,Anterior
• add_slice,t1w.nii.gz: add t1w.nii.gz as the slice
• move_slice,0,20: move sagittal slice (0) to position 20. To move the sagittal slice, use “move_slice,1,20”. To move the axial slice, use “move_slice,2,20”
• slice_on: make slices visible. To enable only sagittal slice, use “slice_on,0”. (0: sagittal, 1: coronal, 2:axial)
• slice_off: make slices invisible. To disable only sagittal slice, use “slice_off,0”. (0: sagittal, 1: coronal, 2:axial)
• set_zoom: set the zoom-in scale. e.g., set_zoom,0.6
• set_stereoscopic: set stereoscopic view
• set_view,0 set_view,1 set_view,2: set the current view to sagittal, coronal, and axial view. Call the same command twice to view from the opposite side (e.g. –cmd=”set_view,2+set_view,2” will view from the top)
• set_roi_view_index: set the background map of the ROI window, e.g. “set_roi_view_index,0” will show the FA or QA map.
• set_param: configure the rendering options. A list of the rendering options can be found at https://github.com/frankyeh/DSI-Studio/blob/master/options.txt For example, the first option is “orientation_convention”, and you may set it to 0 by “set_param,orientation_convention,0” to use Radiology convention

The following commands are for saving a file.

You may specify the file name. For example “add_surface+save_image,file_name.jpg”

• save_image: save a 3D rendering image. The image dimension can be assigned after assigning the file name, e.g., –cmd=”set_view,2+save_image,1.jpg,1024 800”
• save_lr_image: save a left right viewed 3D rendering image.
• save_3view_image, save_h3view_image: save 3D rendering image in 3 views
• save_rotation_video: save a rotation video
• save_roi_image: save the ROI window as an image
• save_mapping: save fa qa or adc mapping as a nifti image
• save_tracks: save current tractography as a trk file. For example, “save_tracks,tracks.tt.gz”

The following commands are for fiber tracking, visualization, and track editing

• save_workspace,/my_work_folder/: save the workspace to a folder. The directory to the folder is specified after the comma
• load_workspace,/my_work_folder/: load the workspace to a folder. The directory to the folder is specified after the comma
• presentation_mode: change the GUI to presentation mode (hide ROI window)
• save_setting,file.ini: save all GUI setting to the file specified
• load_setting,file.ini: load all GUI setting to the file specified
• save_rendering_setting,file.ini: save rendering setting to the file specified
• load_rendering_setting,file.ini: load rendering setting to the file specified
• save_tracking_setting,file.ini: save tracking setting to the file specified
• load_tracking_setting,file.ini: load tracking setting to the file specified
• restore_rendering : restore all rendering settings
• run_tracking: run tracking using the current parameters
• load_track_color,my_track_color_file.txt: load the color for current tract from a text file.
• load_cluster_color,clutser_colors.txt: load the color for all loaded tracts from a text RGB file.
• cut_by_slice: cut tracks by the current slice position. Specify slice orientation by 0:sagittal 1:coronal, 2:axial. and direction by 0:lesser 1:greater. For example, --cut_by_slice,2,1 cut tracks at Z+