Parcelman v1.0:
A tool for manual parcellation of cortical surfaces
Corresponding author:
- 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 (click the image for a full-size view in a new window).
Features:
- Allows painting of either the fiducial (folded) or flattened surface. You draw a region of interest or a line with your mouse; then you select a label value for it.
- Allows painting in the volume associated with the surfaces (a slice-editing replaces the right-hand surface editing module). The surface location and volume locations are linked; editing one changes the other.
- The program can manage up to 255 label values -- you get to choose which 16 of those you wish to work with at any given time. You also have control over the colors assigned to each label. The program supports an optional legend file that associates a name with each label.
- An orthogonal slice viewer module allows you to see where the surface intersects the volume and to navigate through the volume. Within this you can request that the program locate the closest surface location to any volume location.
- Accepts ANALYZE and VAPET storage format volumes. These volumes can be GZIPPED ("gzip" both .hdr and .img files).
- Accepts VTK, OFF and SRF surface formats.
- Supports a statefile that retains filenames and colors
Requirements:
- Requires IDL5.5 or higher as either a development or runtime license. The IDL6.0 Virutal Machine (it's free!) may also be used. Obtain IDL from Research Systems Inc. at http://www.rsinc.com/
- Requires1.0 MBytes for a Save set, and 34 MBytes for the example data. The gzipped tarfile is 10 MBytes.
- Requires a three-button mouse or a graphics tablet and pen. A pen may be more comfortable to use for extended periods.
Release History:
- Save sets are available for IDL versions 5.6 and 6.0. The 6.0 save sets have been verified under Windows 2000 as well as Linux.
- The IDL6.0 save set has been run using an IDL Virtual Machine on Windows 2000 and Linux. An IDL 6.1 Virtual machine also accepts the 6.0 save set.
- No source code is provided as yet; I want to hear from you when there are problems.
Software revisions:
- The current version is 1.0 (October, 2004). This is the initial release.
Notes:
- No testing has been performed on Macintoshes for this package, but other applications developed by this group were compatible with OS 10 systems.
- Filenames with spaces are apt to cause problems, because the primary author became set in her ways long ago!
- There are plans to support MINC and NIFTE formats fairly soon, but for now you must do your own conversions to and from ANALYZE.
How to get it:
- Use this REQUEST FORM to request the software.
Online Help
Click here to get detailed instructions on operation. There is a Help button in the program as well.Reference:
If you use ParcelMan in publications, please cite the following:- Rehm K, Ju L, Stern J, Schaper K, Rottenberg DA. ParcelMan and Pigment: interactive tools for parcellation of cortical grey matter. NeuroImage 22, supplement 1 (HBM2004), A287, 2004.
Cost: US$0.00
Page last updated November 4, 2004.