This command line looks good to me -- unless there is a newline between some of the arguments (e.g., right before ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor). It's impossible to tell this from email, but try copying this whole command line to a text editor, and replace any newlines with spaces. Then cd to the surf subdirectory corresponding to this subject, and paste that command into the terminal window.
There should be 20 arguments, and there are 20 arguments (excluding the option -surface-border-landmark-identification), so it should work. On 04/26/2011 06:41 PM, Colin Davey wrote: > Hi, > > I am trying to run the preborder.sh freesurfer pipline script, on the > "bert" sample data that comes with Freesurfer. > > Line 242 has the following command: > > caret_command -surface-border-landmark-identification $SPACE > $VOLUME_ANATOMY $FIDUCIAL $INFLATED $VINFLATED $ELLIPSOID $TOPO > $GEOGRAPHY_PAINT $GEOGRAPHY_PAINT Geography $SHAPE Depth $AREACOLOR > $AREACOLOR $VOCAB $VOCAB "" $OUTBORDERPROJ "" $BORDERCOLOR > > When running, this translates to: > > caret_command -surface-border-landmark-identification 711-2C-111 > CorpusCallosum.nii.gz deformed_Human.bert.L.Midthickness_711-2B.coord > Human.bert.L.Inflated.73730.coord > Human.bert.L.VeryInflated.73730.coord > Human.bert.L.Ellipsoid.73730.coord Human.bert.L.CLOSED.73730.topo > Human.bert.L.Initial.73730.paint Human.bert.L.Initial.73730.paint > Geography Human.bert.L.Initial.73730.surface_shape Depth > Human.bert.L.Initial.areacolor Human.bert.L.Initial.areacolor > Human.bert.L.Initial.vocabulary Human.bert.L.Initial.vocabulary '' > Human.bert.L.LANDMARKS.borderproj '' > ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor > > and results in the following error message: > > SURFACE BORDER LANDMARK IDENTIFICATION ERROR: Parameter named "Input > Border Color File Name" is missing. > > Any ideas what is going wrong? > > Cheers, > > - C > > > *************************************** > > Colin Davey > > Scientist > > Senior Software Engineer > > > Electrical Geodesics, Inc. > > 1600 Millrace Dr. St 307 > > Eugene, OR 97403 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
