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
>
>
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