But doesn't this require you already have a surface? I'm trying to create a surface from a segmentation volume. In the same way the GUI operation of Volume -> Segmentation -> Reconstruct into surface.
On Fri, Jul 26, 2013 at 2:00 AM, Donna Dierker <donna.dier...@sbcglobal.net>wrote: > Sounds like you have a segmentation already, so don't use -volume-segment. > > Try something like this instead: > > caret_command -surface-identify-sulci $SPECFNAME $HEM $SEGVOL $TOPO > $FIDUCIAL $FIDUCIAL > > --- > caret_command -surface-identify-sulci > <spec-file-name> > <structure> > <segmentation-volume-file-name> > <closed-topology-file-name> > <raw-coordinate-file-name> > <fiducial-coordinate-file-name> > <volume-write-type> > > Identify Sulci with shape and paint. > > Create a surface shape file containing depth and curvature > measurements, > a paint file identifying the sulci, and an area color file. If > there > is no raw coordinate file, specify fiducial coordinate file > instead. > > NOTE: This command MUST be run in the directory containing the > files. > > structure Specifies the brain structure. > Acceptable values are RIGHT or LEFT > > write-volume-type Type of volume files to write. > Specifies the type of the volume files that will be written > during the segmentation process. Valid values are: > AFNI > NIFTI > NIFTI_GZIP (RECOMMENDED!!!!) > SPM > WUNIL > > > On Jul 24, 2013, at 9:14 PM, Tristan Chaplin <tristan.chap...@gmail.com> > wrote: > > > Hi, > > > > I am trying to create a surface from a segmentation volume using the > command line. The anatomy volume was not segmented with Caret. When I do > this: > > > > caret_command -volume-segment "" seg.nii Other.Case.L.spec > NNNNNNYYNNNNNNNNN 1 0 NNNNNN LEFT SUREFIT_THEN_GRAPH NIFTI_GZIP > > > > I get: > > > > VOLUME SEGMENTATION ERROR: Unable to find volume file > "RadialPositionMap+orig.*" > > > > I also get the same error when using the GUI, Volume -> Segmentation > Operations (Surefit) ... > > > > But if I use the GUI and use Volume -> Segmentation -> Reconstruct into > surface, it works. > > > > I'm using Caret 5.65 on OSX 10.8.4. Any ideas why this is happening? > > > > Cheers, > > Tristan > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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