OK, done! On Apr 29, 2011, at 9:15 AM, Donna Dierker wrote:
> 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
