Hi Donna, Thanks, but that -volume-segment command is what I tried in the first email and it produces the error I mentioned. It appears there is no command equivalent for the GUI Volume -> Segmentation -> Reconstruct into surface, I'll just have to work around it for now.
Cheers, Tristan On Mon, Jul 29, 2013 at 11:58 PM, Donna Dierker <do...@brainvis.wustl.edu>wrote: > Yes, I think it does require a surface as input. You can generate it in > the GUI, like you cite below, or you can see if you can get this to work, > toggling off 1-6 and toggling on what you need in 7-17. I never used this > much, and I'm not sure it will work in your case, but the fact that it > takes an input segmentation volume is encouraging. > > caret_command -volume-segment > <input-anatomy-volume-file-name> > <input-segmentation-volume-file-name> > <spec-file-name> > <operation-code> > <gray-peak> > <white-peak> > <padding-code> > <structure> > <error-correction-method> > <write-volume-type> > > Perform segmentation operations. > > Operation_Code characters > Specify each with either a "Y" or "N". > All characters must be specified. > Character Operation Description > --------- --------------------- > 1 Disconnect Eye and Skull > 2 Disconnect Hindbrain > 3 Use High Threshold for Hindbrain > disconnection > 4 Cut Corpus Callossum > 5 Generate Segmentation > 6 Fill Ventricles > 7 Generate Raw and Fiducial Surfaces > 8 Reduce polygons in surfaces > 9 Correct topological errors in surfaces > 10 Generate Inflated Surface > 11 Generate Very Inflated Surface > 12 Generate Ellipsoid Surface (For Flattening) > 13 Generate Spherical Surface > 14 Generate Comp Med Wall Surface > 15 Generate Hull Surface > 16 Generate Curvature, Depth, and Paint > Attributes > 17 Generate Registration and Flattening > Landmark Borders > > gray-peak specifies the intensity of the gray matter peak > in the > anatomy volume. > > white-peak specifies the intensity of the white matter > peak in the > anatomy volume. > > padding-code > Specify padding for any cut faces when segmenting a > partial hemisphere. > Specify each with either a "Y" for padding or "N" for no > padding. > All characters must be specified. > Character Padding Description > --------- ------------------- > 1 Pad Negative X > 2 Pad Positive X > 3 Pad Posterior Y > 4 Pad Anterior Y > 5 Pad Inferior Z > 6 Pad Superior Z > > structure Specifies the brain structure. > Acceptable values are RIGHT or LEFT > > spec-file-name Name of specification file. > > input-anatomy-volume-file-name > If there is not an anatomy volume file, leave this > item blank (two consecutive double quotes). > > input-segmentation-volume-file-name > If there is not a segmentation volume file, leave this > item blank (two consecutive double quotes). > > error-correction-method > NONE > GRAPH > SUREFIT > SUREFIT_THEN_GRAPH > GRAPH_THEN_SUREFIT > > 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 > > All input volumes must be in a Left-Posterior-Inferior > orientation > and their stereotaxic coordinates must be set so that the > origin is > at the anterior commissure. > > > On Jul 28, 2013, at 10:31 PM, Tristan Chaplin <tristan.chap...@gmail.com> > wrote: > > > 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 > > > > _______________________________________________ > > 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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