No newline. I'm just running the preborder.sh freesurfer pipline script, as downloaded, only changing the environment variable lines at the beginning as instructed. I get the same message in the context of running the entire script, or pasting it directly into the terminal.
I'm using freesurfer version 5 on a Mac, if that helps. On Apr 27, 2011, at 7:49 AM, Donna Dierker wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
