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 <[email protected]> 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 <[email protected]>
> 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 <[email protected]>
> 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
> > [email protected]
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
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