You're right: I don't see any newlines. I'm trying this on my end (running it on bert), albeit with different pathnames.
Could you run it lke so: preborderBert.sh >& preborderBert.out.txt Then upload preborderBert.out.txt so I can see the results of every line executing. On 04/28/2011 02:56 PM, Colin Davey wrote: > 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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
