
Usage: freeview [OPTION <ARGUMENT:SUB-OPTION>]...
Volume and surface viewer and editor for freesurfer.

-v, --volume <FILE>...
       Load one or multiple volume files. Available sub-options are:

       ':colormap=name' Set colormap for display. Valid names are
       grayscale/lut/heat/jet/gecolor/nih/pet/binary.

       ':grayscale=min,max' Set grayscale window values.

       ':heatscale=min,mid,max' Set heat scale values. If only 2 values given,
       min and mid will be set to the same value.

       ':heatscale_options=option1[,option2]' Set heat scale options. Options
       can be 'truncate','invert', or both.

       ':heatscale_offset=val' Set heat scale offset value.

       ':colorscale=min,max' Set generic colorscale values for
       jet/gecolor/nih/pet.

       ':lut=name' Set lookup table to the given name. Name can be the name of
       a stock color table or the filename of a color table file.

       ':binary_color=color' Set the color of the non-zero voxels. Colormap
       must be set to binary. Color can be a color name such as 'red' or 3
       values as RGB components of the color, e.g., '255,0,0'.

       ':percentile=flag' Set min/mid/max thresholds as percentile.

       ':vector=flag' Display 3 frame volume as vectors. flag can be 'yes',
       'true' or '1'.

       ':tensor=flag' Display 9 frame volume as tensors. flag can be 'yes',
       'true' or '1'.

       ':vector_width=width' Set line width of the vectors.

       ':vector_norm_threshold=value' Set norm threshold for the vector
       display.

       ':vector_skip=n' Skip n voxels in vector display. Default is 0 (no
       skipping).

       ':vector_normalize=flag' Normalize vector length. flag can be 'yes',
       'true' or '1'.

       ':vector_scale=scale' Set the length scale of the vectors.

       ':render=flag' When displaying as vectors or tensors, render the glyph
       in the given form. For vector, flag can be 'line' as simple line,
       'directional' as directional line and 'bar' as 3D bar (might be slow).
       For tensor, flag can be 'boxoid' or 'ellipsoid' (slow!).

       ':inversion=flag' When displaying as vectors or tensors, invert the
       given component of the vectors. Valid flags are 'x', 'y' and 'z'.

       ':outline=flag' Display labels as outline only. flag can be '1', 'yes'
       or 'true'.

       ':reg=filename' or ':transform=filename' Set registration/transform
       file for the volume. filename can contain relative path to the volume
       file.

       ':resample=method' or 'interpolation=method' Set the interpolation
       method when resampling is necessary. method can be 'nearest' (default),
       'trilinear' or 'cubic.

       ':opacity=value' Set the opacity of the volume layer. value ranges from
       0 to 1.

       ':mask=volume_name' Use the given volume to as mask for display. The
       mask volume must be loaded first.

       ':isosurface=low_threshold,high_threshold' Set 3D display as
       isosurface. High_threshold is optional. If no threshold or simply 'on'
       is given, threshold will be either automatically determined or
       retrieved from the save previously settings.

       ':isosurface_color=color' Set the color of the isosurface. Color can be
       a color name such as 'red' or 3 values as RGB components of the color,
       e.g., '255,0,0'.

       ':isosurface_smooth=iterations' Set the number of smooth iterations.
       Default value is 5.

       ':extract_all_regions=flag' Set isosurface to extract all regions.
       default setting is on.

       ':isosurface_output=filename' Save isosurface to file. Extension can be
       .vtk or .stl.

       ':surface_region=file' Load isosurface region(s) from the given file.
       isosurface display will automatically be turned on.

       ':name=display_name' Set the display name of the volume.

       ':lock=lock_status' Lock the volume layer so it will not be moved in
       the layer stack. Status can be '1' or 'true'.

       ':linked=flag' Link the volume layer with other linked volumes. Flag
       can be '1' or 'true'.

       ':visible=visibility' Set the initial visibility of the volume.
       Visibility can be '1' or '0' or 'true' or 'false'.

       ':smoothed=flag' Set smoothed display for the volume. Flag can be '1'
       or '0' or 'true' or 'false'.

       ':rgb=flag' Display 3-frame volume in RGB color. Voxel values must be
       in the range of 0~255. Flag can be '1' or '0' or 'true' or 'false'.

       ':structure=name_or_value' Move the slice in the main viewport to where
       it has the most of the given structure.

       ':ignore_header=flag' Ignore header information. Use the existing
       volume's header info. Flag can be '1' or '0' or 'true' or 'false'.

       ':frame=number' Set active frame (0 based).

       ':auto_adjust_frame_contrast=flag' Set flag for automatically adjust
       frame contrast. Flag can be '1' or 'true'.

       ':select_label=label_index' When colormap is set as look up table,
       select and show only the given labels. Multiple labels can be given
       separated by comma, such as, '5,10,20'.

       Example:
       freeview -v T1.mgz:colormap=heatscale:heatscale=10,100,200

-r, --resample
       Resample oblique data to standard RAS.
-conform, --conform
       Conform the volume to the first loaded volume.
-trilinear, --trilinear
       Use trilinear as the default resample method.
-cubic, --cubic
       Use cubic as the default resample method.
-smoothed, --smoothed
       Use smoothed display as the default display method for volumes.
-colormap, --colormap <TYPE>
       Use the give colormap type as the colormap for all the volumes to be
       loaded after.
-dti, --dti <VECTOR> <FA>...
       Load one or more dti volumes. Need two files for each dti volume. First
       one is vector file. Second one is FA (brightness) file.
-tv, --tract-volume <FILE>...
       Load one or more tract volumes.Available sub-options are:

       ':frame=frame_number' Show only a single tract by frame number.

-f, --surface <FILE>...
       Load one or multiple surface files. Available sub-options are:

       ':curvature=curvature_filename' Load curvature data from the given
       curvature file. By default .curv file will be loaded if available.

       ':curvature_method=method' method to display curvature. available
       options are 'off', 'binary' or 'threshold'. default is 'threshold'.

       ':curvature_setting=midpoint,slope' method to set curvature midpoint
       and slope.

       ':overlay=overlay_filename' Load overlay data from file.

       ':overlay_reg=overlay_registration_filename' Apply registration when
       loading overlay data.

       ':overlay_method=method_name' Set overlay method. Valid names are
       'linear', 'linearopaque' and 'piecewise'.

       ':overlay_color=colorscale,settings' Set overlay color setttings. Valid
       names are 'colorwheel', 'truncate', 'inverse', 'clearlower' and
       'clearhigher'. Use comma to apply more than one. 'clearlower/higher'
       only works when overlay_custom option is on.

       ':overlay_custom=[filename]val,r,g,b,val2,r2,g2,b2...' Set customized
       overlay color. If only given one argument as filename, customized color
       scale will be loaded from the given file.

       ':overlay_opacity=opacity' Set opacity of overlay.

       ':overlay_threshold=low,(mid,)high(,percentile)' Set overlay threshold
       values, separated by comma. When overlay method is linear or
       linearopaque, only 2 numbers (low and high) are needed. When method is
       piecewise, 3 numbers are needed. If last element is 'percentile', use
       the give numbers as percentile.

       ':overlay_mask=filename(,invert)' Use given label file as mask for
       overlay. If invert is specified, use the inverted mask.

       ':overlay_frame=frame_number' Set active frame of multi-frame overlay.

       ':overlay_smooth=smooth_steps' Set smooth steps for overlay.

       ':overlay_zorder=number' Set z-order for rendering overlay.

       ':mrisp=filename' load parameterization data from file as overlay.

       ':sphere=filename' load given sphere file.

       ':patch=patch_filename' Load given patch file.

       ':correlation=correlation_filename' Load correlation data from file.
       Correlation data is treated as a special kind of overlay data.

       ':color=colorname' Set the base color of the surface. Color can be a
       color name such as 'red' or 3 values as RGB components of the color,
       e.g., '255,0,0'.

       ':opacity=value' Set surface opacity. Value ranges from 0 to 1.

       ':edgecolor=colorname' Set the color of the slice intersection outline
       on the surface. If set to 'overlay', will use overlay color

       ':edgethickness=thickness' Set the thickness of the slice intersection
       outline on the surface. set 0 to hide it.

       ':affinexfm=filename' apply affine xfm LTA to the surface vertex xyz
       (automatically determines proper direction and converts to tkreg)

       ':annot=filenames' Set annotation files to load.

       ':annot_outline=flag' Show surface annotation as outline. flag can be
       'true', 'yes' or '1'.

       ':annot_zorder=number' Set z-order for rendering annotation.

       ':name=display_name' Set the display name of the surface.

       ':offset=x,y,z' Set the position offset of the surface. Useful for
       connectivity display.

       ':visible=visibility' Set the initial visibility of the surface.
       Visibility can be '1' or '0' or 'true' or 'false'.

       ':vector=filename' Load a vector file for display.

       ':target_surf=filename' Load a target surface file for vectors to
       project on for 2D display.

       ':label=filename' Load a surface label file.

       ':label_outline=flag' Show surface labels as outline. flag can be
       'true', 'yes' or '1'.

       ':label_color=colorname' Set the color of the surface label.

       ':label_centroid=flag' Move 3D cursor to the centroid of the label.
       flag can be 'true', 'yes' or '1'.

       ':label_visible=flag' Set label visibility.

       ':label_opacity=value' Set label opacity. Value ranges from 0 to 1.

       ':label_threshold=value' Set label threshold.

       ':label_zorder=number' Set z-order for rendering labels.

       ':spline=filename' Load a spline file for display.

       ':vertex=flag' Show surface vertices on both 2D and 3D views. flag can
       be 'true', 'on' or '1'.

       ':vertexcolor=colorname' Set color of the vertices. Color can be a
       color name such as 'red' or 3 values as RGB components of the color,
       e.g., '255,0,0'.

       ':goto=vertex_number' Move the cursor to the given vertex and center
       the view around it.

       ':hide_in_3d=flag' Hide surface in 3D view. flag can be 'true', 'on' or
       '1'.

       ':all=flag' Indicate to load all available surfaces. flag can be
       'true', 'yes' or '1'.
       ':no_shading=flag' Indicate to set the ambient coefficient of the
       surface to full strenge so that there will be no shading effect
       rendered. flag can be 'true', 'yes' or '1'.

-edgecolor, --edgecolor <color>
       Use the give color as the edge color for all the surfaces to be loaded
       after.
-l, --label <FILE>...
       Load one or multiple label(ROI) files. Available sub-options are:

       ':ref=ref_volume' Enter the name of the reference volume for this label
       file. The volume is one of the volumes given by -v option.

       ':color=name' Set color of the label. Name can be a generic color name
       such as 'red' or 'lightgreen', or three integer values as RGB values
       ranging from 0 to 255. For example '255,0,0' is the same as 'red'.

       ':opacity=value' Set the opacity of the label. value ranges from 0 to
       1.

       ':threshold=value' Set the threshold of the label.

       ':centroid=flag' Move the cursor to the centroid of the label. flag can
       be '1', 'true' or 'yes'.

-w, --way-points <FILE>...
       Load one or multiple way points files. Available sub-options are:

       ':color=name' Set color of the way points. Name can be a generic color
       name such as 'red' or 'lightgreen', or three integer values as RGB
       values ranging from 0 to 255. For example '255,0,0' is the same as
       'red'.

       ':splinecolor=name' Set color of the spline.

       ':splineheatmap=filename,min,mid,max' Set heatmap data file to load and
       heatmap settings for the spline.

       ':radius=value' Set radius of the way points.

       ':splineradius=value' Set radius of the spline tube.

       ':name=display_name' Set the display name of the way points.

       ':visible=visibility' Set the initial visibility of the way points.
       Visibility can be '1' or '0' or 'true' or 'false'.

-c, --control-points <FILE>...
       Load one or multiple control points files. Available sub-options are:

       ':color=name' Set color of the control points. Name can be a generic
       color name such as 'red' or 'lightgreen', or three integer values as
       RGB values ranging from 0 to 255. For example '255,0,0' is the same as
       'red'.

       ':radius=value' Set radius of the control points.

       ':name=display_name' Set the display name of the control points.

       ':visible=visibility' Set the initial visibility of the control points.
       Visibility can be '1' or '0' or 'true' or 'false'.

       ':new' if cannot find the file, create a new one with the given
       filename.

-p-labels, --p-labels <FILES>...
       Load multiple p-label volume files.

-p-prefix, --p-prefix <PREFIX>...
       Set the file name prefix for p-label volume. program will use this to
       figure out label name from file name.

-p-lut, --p-lut <NAME>...
       Set the look up table name to use for p-label display. name can be the
       name of a stock lookup table or the file name of a lookup table file.
       default is the default freesurfer look up table.

-cmat, --connectome-matrix <CMAT_FILE> <PARCELLATION_FILE>
       Load connectome matrix data files. Requires a cmat file and a
       parcellation volume file. Available sub-options are:

       'lut=color_table' Enter the name or file name of the color table to be
       used. Default is the FreeSurfer default LUT.

-fcd, --fcd <SUBJECT_DIR> <SUBJECT> [SUFFIX]
       Load FCD data. Requires subject directory and subject. Suffix is
       optional.

-t, --tract <FILE>...
       Load one or more tract files.

-tc, --tract-cluster <DIRECTORY>
       Load tract cluster data from given directory.

-odf, --odf <FILE> [Vertex_file] [Face_file]
       Load ODF data. If no vertex and face files given, will use the default
       vertices and faces by Diffusion Toolkit. Available sub-options are:

       ':permuted=1' Indicates that the odf data is permuted. Odf data from
       DTK is permuted.

-recon, --recon <SUBJECT_NAME>...
       Load a series of pre-defined volumes and surfaces of given subject(s).

-lineprofile, --lineprofile <OUTPUT_FILE>
       Compute the thickness of layers along line profiles and export them to
       given csv file. Initial lines (waypoints) must be loaded in order with
       waypoint options. Available sub-options are:

       ':spacing=value' Set spacing of the line profiles. Default value is
       1.0.

       ':resolution=value' Set resolution of the line profiles. Default value
       is 1.0.

       ':offset=value' Set the offset to compute line profiles. Default value
       is 5.

       ':segments=value' Set the number of segments on the line profiles.
       Default value is 100.

-ss, --screenshot <FILENAME> <MAGNIFICATION_FACTOR> <AUTO_TRIM>
       Take a screenshot of the main viewport and then quit the program.
       Default value for magnification factor is 1. AUTO_TRIM can be
       'autotrim', 'true' or '1'. To automatically cycle through all the
       volumes/surfaces, put '%name' in the filename as the wildcard for layer
       name.
-layout, --layout <STYLE>
       Set layout of the view panels as given. Accepted styles are 1, 2, 3 &
       4. 1 is single panel. The rest are 3 different 4-panel styles.
-view, --view <VIEW>
       Set the 3D view as given. Accepted views are 'left', 'right',
       'lateral', 'medial', 'anterior', 'posterior', 'inferior' and
       'superior'. 'lateral' and 'medial' will only work when there is visible
       surface.
-viewport, --viewport <NAME>
       Set the main viewport as given. Accepted names are 'sagittal' or 'x',
       'coronal' or 'y', 'axial' or 'z' and '3d'.
-viewsize, --viewsize <width> <height>
       Set the size of the main viewport. The size of the whole window will be
       changed accordingly.
-zoom, --zoom <FACTOR>
       Set zoom factor of the main viewport.
-cam, --camera <OPERATION1> <FACTOR1> <OPERATION2> <FACTOR2>...
       Set a series of camera operations for the 3D view. Valid operations
       are:

       'Azimuth' Rotate the camera about the view up vector centered at the
       focal point. The result is a horizontal rotation of the camera.

       'Dolly' Divide the camera's distance from the focal point by the given
       dolly value. Use a value greater than one to dolly-in toward the focal
       point, and use a value less than one to dolly-out away from the focal
       point.

       'Elevation' Rotate the camera about the cross product of the negative
       of the direction of projection and the view up vector, using the focal
       point as the center of rotation. The result is a vertical rotation of
       the scene.

       'Roll' Rotate the camera about the direction of projection. This will
       spin the camera about its axis.

       'Zoom' Same as 'Dolly'.

       Note that the order matters!

       For example: '-cam dolly 1.5 azimuth 30' will zoom in the camera by 1.5
       times and then rotate it along the view up vector by 30 degrees.

-orthographic, --orthographic
       Set orthographic projection for 3D view.
-ras, --ras <X> <Y> <Z> [Option]
       Set cursor location at the given RAS coordinate. If option is given as
       'tkreg', the entered coordinate is in tkreg coordinate.
-slice, --slice <X> <Y> <Z>
       Set cursor location at the given slice numbers of the first loaded
       volume.
-cc, --center-at-cursor
       Center the view at cursor location.
-timecourse, --timecourse
       Show time course window.
-transform-volume, --transform-volume
       Show transform volume window.
-colorscale, --colorscale
       Show color scale bar on the main view.
-write-slice-intersection, --write-slice-intersection <plane> <filename_format> <start> <end>
       Save polylines of the surface intersected by slice. plane can be
       sag/cor/hor.
-cmd, --command <FILE>
       Load freeview commands from a text file.
-hide, --hide <LAYER_TYPE>
       Hide the current layer. This is useful for loading comands by -cmd
       option. Valid LAYER_TYPEs are volume, surface, label, etc.
-unload, --unload <LAYER_TYPE>
       Unload/Close the current layer. Useful for loading comands by -cmd
       option. Valid LAYER_TYPEs are volume, surface, label, etc.
-rorder, --reverse-order
       Load layers in reversed order.
-nocursor, --nocursor
       Hide the cursor.
-hide-3d-slices, --hide-3d-slices
       Hide slices in 3D view.
-hide-3d-frames, --hide-3d-frames
       Hide slice frames in 3D view.
-hide-x-slice, --hide-x-slice
       Hide x slice in 3D view.
-hide-y-slice, --hide-y-slice
       Hide y slice in 3D view.
-hide-z-slice, --hide-z-slice
       Hide z slice in 3D view.
-subtitle, --subtitle <TEXT>
       Add subtitle to freeview window caption.
-auto-load-surf, --auto-load-surf
       Do not automatically load sphere or other supplemental surface data.
-sync, --sync-cursor
       Sync cursor position across freeview instances.
-quit, --quit
       Quit freeview. Useful for scripting or loading comands by -cmd option.
-noquit, --noquit
       Do not quit freeview after screenshot command.
-stdin, --stdin
       Listening stdin for freeview command sent by other programs.
-verbose, --verbose
       Print out a lot more information, such as vertex coordinate of each
       click, etc.
-prefix, --prefix <prefix> <filename>
       Add prefix to the volume names of the given filenames
-continue, --continue
       Continue as far as possible if an error occured
-h, --help
       Display this help.
