Parcelman V1.0:
A tool for manual parcellation of cortical surfaces
Corresponding author:
ParcelMan: Download | Help
- What it does:
ParcelMan allows you to manually label a structural volume and its associated surfaces. If you label a surface the labels are transfered to the volume and vice-versa.
See the screenshot below for an idea of the interface layout.
GENERAL INFORMATION
You have the option to supply two surfaces. The coordinates of vertices in surface 1 MUST be directly interpretable as coordinates in the MRI volume! The second surface can only differ from the first in the position of the vertices.
The surface meshes are expected to consist of triangles and the number and order of the triangles must be the same for any pair of surfaces. A typical surface pair is one folded and one spherically-mapped surface or grey-matter and white-matter surfaces.
ParcelMan is designed to keep volume and surface labels synchronized as much as possible. This is done via a massive look up table (called a "Pigment" file) that explicitly links triangle numbers and voxels. If you do not have such a file, the program will compute a simple-minded one from Surface 1.
WHENEVER you perform a volume edit, the voxels you change will also change the triangles they influence. The reverse is true when editing triangle labels.
THE INTERFACE
The package consists of 4 subsections. On the left a subwidget area appears labelled SURFACE 1 EDITOR. On the right there are three subwidgets accessible by tabs. The first is SURFACE 2 EDITOR, which is almost identical to the surface 1 editor. The next tab displays Orthogonal Slices through the volume. This subwidget only allows navigation, not editing. The third tab brings up the Slice Editor which allows you to paint on whichever slice you please. You will be able to paint volume voxels that do not involve the surface, or confine yourself only to voxels touching the surface.Top-Level buttons
- EXIT writes out the current surface and volume labels to the filenames that were specified (see Load Files). This action will OVERWRITE existing file contents.
- QUIT exits without changing original file contents.
- Load Files brings up an interface for selection/entry of filenames STATIC files (some of which are optional) are pre-existing volumes and surfaces that describe the brain you are working on. DYNAMIC files contain the numeric labels that have anatomical "meaning" for the surface and volume. They will be created with a uniform value of 1 if they do not yet exist. Backup versions of the specified files will be created with their contents at the time they are read in/created. When you Get Files everything is read in (this is often slow). If you have already loaded all the STATIC files, you can use Get just the LABEL files to swap to different labelling schemes. You will get a little text window to let you know the load progress.
- Read Statefile [/Write Statefile] is a drop-down menu. If you expect to carry out multiple editing sessions on the same brain, use Write Statefile to save all the filenames and the colors you have selected. Read Statefile will load those colors and set those filenames as the initial values seen in Load Files. NOTE: You still have to go through Load Files to get your data in!
- SAVE current labels will ask whether you want to save the current labels using the original filenames OR will allow you to type in new names.
- UNDO last edit does just that. Both triangle and volume labels revert to their values prior to the last edit (it does not matter whether the editing took place on a surface or a slice).
- Color controls brings up an interface where you may adjust the brightness and contrast of the anatomical slice or surface. You may also adjust the color that corresponds to any numeric label. Select a label by number (or name, if you supplied a "legend" file in Load Files). The small colortab windows will be updated immediately, but the labels as shown on the surfaces and slices will not be updated until you are DONE.
- Label control will bring up a window where you may select up to 16 label numbers to assign to the working set of buttons in the editing windows. If you specify less than 16 numbers, those you choose will show up beginning at the left.
- Debug Off [/Debug On] A new "Parcelman.journal" text file is created each time you launch ParcelMan. Debug On will cause much more stuff to be printed there in case you need to send a bug report to the author.
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Loading files
Click Load Files and you will get an interface like the one below. The STATIC files must already exist, although you do not need all of them. The minimum that you do need is an MRI volume and an unflattened surface. For all other files, use NULL as the filename or clear out the field if you don't want to use them. You can either type in the fields or use the browser to fill them.
The DYNAMIC files are the ones
that will contain the labels you assign. The program will create
files if you do not supply existing files. The label volume is a
byte volume of the same dimensions as the MRI volume. The triangle
labelfile contains one label per triangle. It is an ascii file.
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Surface Editor controls
If you only supplied one surface, it will appear in both windows.
If you do supply a second surface and it seems to be flattened,
the program will attempt to orient it so the front and top vertices in
Surface 1 maintain their relative positions. This logic is not 100%
successful, however.
Below the graphics window are 16 color boxes showing the color associated with the 16 current labels below. Once you have defined a ROI or Line (see Mouse Actions below), you MUST click on the label to be assigned to it. Nothing will happen otherwise!
Surface rotation is managed by sliders marked Longitude, Latitude and Anti-clockwise twist. The latter should only be necessary if the surface appears upside down.
- UPDATE VIEW will force a refresh of the display, bringing up the current labels and erasing any regions of interest (ROIs) or lines drawn on the surfaces.
- Set View menu will bring up views standard longitudes and latitudes or bring the marked triangle front and center.
- Set Zoom allows zooming in and out. Pan by using the scrollbars on the window itself.
- ACTION: manages what you will do with your mouse to edit labels on the surface. Lines widths are expessed in mm for Surface 1, although the effect is to select those triangles covered by the line. For large triangles the resulting appearance may be jagged. You may also redraw the most recent ROI or line. ROIs and lines are retained as screen coordinates -- if you change the rotation or zoom factor of the surface they will not be where you expect!
- TOGGLE LABELS goes back and forth between showing a greyscale rendering of the surface (with a lighting model for Surface 1; Surface 2 controls allow two other choices of precomputed labels, for example, curvature.)
- TOGGLE MARK lets you hide it. You can not change its size.
- Save Picture will take the full contents of the window and save them as a truecolor TIFF.
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Slice Editor controls
Below the graphics window are 16 color boxes showing the color
associated with the 16 current labels below. Once you have defined a ROI
or Line (see Mouse Actions below), you MUST click on the label to be
assigned to it. Nothing will happen otherwise!
- Move through the slices using the + 1 slice and - 1 slice buttons.
- You may switch between Axial,Coronal and Sagittal slices through the volume; volume orientation is extracted from the MRI volume header -- the substring on the buttons tells you which direction you will go by moving +1 slice.
- Set Zoom allows zooming in and out. Pan by using the scrollbars on the window itself.
- Delete ROI assigns a value of zero to the ROI (or line).
- Redraw current ROI does just that. The ROI stays current whether you redraw it or not -- which means it can be reused on another slice.
- Edit tool: manages what you will do with your mouse to edit labels on the slice. Line widths are expessed in mm, although you are not guaranteed to get exactly the same effect at different zoom factors.
- Ordinary editing [/Parcellation] toggles between the plain mode, where all selected voxels can be labelled and the special mode where ONLY voxels which are ALREADY labelled can be changed. This is very convenient for adjusting surface labels by changing volume labels -- you need not draw so carefully!
- Show Label allows you to select one or all of the current working labels to show. When parcellating, you could use this trick to change all of label 5 to label 4 with one large roi repeatedly applied over all slices.
- REFRESH will force a refresh of the display, bringing up the current labels and erasing any regions of interest (ROIs) or lines drawn on the surfaces.
- TOGGLE LABELS has three modes here: the first is a color fusion, the second shows just the slice, and the third shows the labels as fully opaque.
- TOGGLE CROSSHAIR will turn the mask on and off (if you provided a mask).
- SET MARK will compute the nearest surface voxel to the point of intersection and the mark on the surface renderings will move to the new location. The rotations of the surfaces will remain unchanged, however.
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Mouse Actions
This program was designed for a 3-button mouse! Use Alt or CTRL keys if need be.- Ordinary Mode:
- Drawing Mode:
Left-click on a SURFACE Editor rendering sets the mark, which is also translated into volume coordinates.
Left-click on a SLICE view merely sets the volume coordinates -- you must force a lookup of the nearest surface location if you want that.
Center-click on a rendering or on the slice to activate Draw Mode (the cursor will change, usually to a pencil)
Left-click sets a point on the outline of a ROI or a line (Left-click and drag will draw a continous line)
Center-click -- WHILE you are in edit mode will undo the last point you set (its former location will still show as black)
Right-click ends the drawing session. A ROI is automatically closed.
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Orthogonal slice viewer controls
You only get to use this module for navigating through the volume. Above the graphics window are two lines of text that tell you how
the program interpreted the volume storage. In this illustration
the storage is "rlapis" which means from voxel number 0,0,0 the first
index goes from right to left, the second from anterior to posterior,
and the third from inferior to superior. Based on this
interpretation, the sliders are annotated with the correct strings, and
an "L" is drawn at the left
side of the axial slice.
- TOGGLE LABELS has three modes here: the first is a fusion, the second shows just the slice, and the third shows the labels as fully opaque.
- TOGGLE CROSSHAIR shows you the point of intersection.
- TOGGLE MASK will turn the mask on and off (if you provided a mask).
- SET MARK will compute the nearest surface voxel to the point of intersection and the mark on the surface renderings will move to the new location. The rotations of the surfaces will remain unchanged, however.
Page last updated November 4, 2004.