Could you upload your preborder.sh here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi
I suspect that when you edited preborder.sh, perhaps some carriage returns or other non-printing character got inserted. Alternatively, in the same directory where preborder.sh is located, do this: cat preborder.sh | tr -d "\r" > /tmp/preborder.sh mv /tmp/preborder.sh preborder.sh chmod 755 preborder.sh This strips any carriage returns from preborder.sh, but leaves newlines intact. On 04/27/2011 03:57 PM, Colin Davey wrote: > 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
