jvs:fscan:manual:chapter2:surface
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jvs:fscan:manual:chapter2:surface [2011/12/19 22:05] – voyvodic | jvs:fscan:manual:chapter2:surface [2012/02/03 19:55] – voyvodic | ||
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**fScan Reference Manual, Chapter 2 (CmdLineOptions): | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
- | ===== Surface -- Surface data===== | + | ===== Surface -- Create and manipulate |
- | + | **usage:**\\ | |
- | + | *-surface surffile --> open SURFFILE in new window -- same as " | |
- | **Version1: | + | *-surface same surffile --> open SURFFILE in same window as IO_IN\\ |
- | Specify surface data options. The meaning of the arguments depends on the MODE. The MODE can be | + | *-surface create fname color imin imax flag dotsize |
- | entered as a number or (more commonly) as a text word. When entering the mode as a text word the | + | *-surface stereo\\ |
- | quotation marks are optional. The default MODE value is -1 (no MODE specified). The meaning of the MODE is as follows: | + | *-surface buffer\\ |
- | * < | + | *-surface merge\\ |
- | * FLG - Used to specify display options: | + | *-surface volume\\ |
- | * 1 - Display fast surface only (if available) | + | *-surface grow volname cnt flag gradient maxcurv wid --> grow surf using images in VOLNAME (if present)\\ |
- | * 2 - Display vertices as dots, don't draw triangles | + | *-surface window\\ |
- | * 4 - Display triangles as wire frame (edges only, don't fill) | + | *-surface join fname --> add fname to current surface\\ |
- | + | *-surface join fname 2 --> add FNAME as second (' | |
- | Note: if INFILE (fScan' | + | *-surface reduce name flag --> make a new dataset by downsampling 3D data |
- | + | ||
- | * new - A new window will be created for this surface; otherwise the surface is drawn in the same window as the previous surface. NEW is assumed for the first surface drawn. This is the first -surface option; in this case the option is used to specify the remaining arguments for the first surface. (Entering 0 for the MODE is the same as ' | + | |
- | * paint - The SURFFILE argument is a PAINT file (see below) rather than a new surface. The paint file is added as a coloring overlay to the most recently specified surface. | + | |
- | * paintall - Like ' | + | |
- | * window - This can be used to set global parameters for a surface window. If WINNUM is specified it is the number of the surface window of interest (0 is first), otherwise the most recent window of the most recently spefifed surface will be assumed. The NAME parameter will be used as the window title. The FLAG parameter sets global flags for the window, as: | + | |
- | * 1 - Display fast surface only (if available) | + | |
- | * newpaint - The SURFFILE argument is the name of a PAINT file to be created during this session. | + | |
- | * create | + | |
- | * COLOR - The COLOR argument can be used to specify the color of the surface data. It can be entered as a 24-bit RGB value explicitly, or by using one of the following color names: | + | |
- | * black | + | |
- | * white | + | |
- | * gray | + | |
- | * red | + | |
- | * green | + | |
- | * blue | + | |
- | * yellow | + | |
- | * orange | + | |
- | * purple | + | |
- | * cyan | + | |
- | * pink | + | |
- | * brown | + | |
- | * IMIN, IMAX - IMIN and IMAX are intensity thresholds; each input voxel with intensity >= IMIN and %%<=%% IMAX will be included in the surface. | + | |
- | * FLAG - The FLAG argument is a bit flag used to specify options: | + | |
- | | + | |
- | * 020 - set vertex colors from voxel intensities) | + | |
- | * 040 - vertex height (Zvalue) is based on voxel intensity | + | |
- | * 0100 - no triangles (save vertices only, don't create triangles) | + | |
- | * 0200 - no smoothing (don't smooth voxel surface cubes) | + | |
- | * 0400 - no border (includes all voxels, not just border voxels) | + | |
- | * output - Allows for rendered views to be saved to disk. In this case FILESPEC is a filename prefix for creating TIFF files (e.g. " | + | |
- | * PAINTFILE - File(s) containing surface parameter data, 1 value per vertex, to paint on the surface. Multiple files can be listed. | + | |
- | + | ||
- | In each surface window there is a separate transformation matrix for each surface, as well as a | + | |
- | global tranformation matrix for the window as a whole. | + | |
- | + | ||
- | + | ||
- | **Version2:**\\ | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | -surface | + | |
- | | + | |
- | | + | |
- | | + | |
paint, paintall, nocolor, newpaint, window, draw, align, append, nofast, grow | paint, paintall, nocolor, newpaint, window, draw, align, append, nofast, grow | ||
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* ASCII files created by the FreeSurfer utility MRIS_CONVERT (from Harvard MGH) | * ASCII files created by the FreeSurfer utility MRIS_CONVERT (from Harvard MGH) | ||
* ASCII surface descriptor files (fScan format) | * ASCII surface descriptor files (fScan format) | ||
- | * Binary surface data files (fScan format) | + | * Binary surface data files (fScan |
+ | * VTK binary surface data files (e.g. Medinria) | ||
+ | * TRK binary fiber tracking data files (from DTK, TrackVis) | ||
+ | |||
+ | [[jvs: | ||
**See Also:**\\ | **See Also:**\\ |
jvs/fscan/manual/chapter2/surface.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1