Hi Donna, > cat preborder.sh | tr -d "\r" > /tmp/preborder.sh > mv /tmp/preborder.sh preborder.sh > chmod 755 preborder.sh
I've run this code, and am still getting the same error. I've uploaded the file. It's called preborderBert.sh. On Apr 28, 2011, at 8:30 AM, Donna Dierker wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
