Hmmm. I run that pipeline, using bert -- albeit with Linux version 5.615, which is what I happen to have installed -- and it works just fine. I even confirm I get exactly the same command line that you get. AND I stepped through your output, and I can't see where anything failed prior to that step, which is what I expected to see.
I'm going to have to try installing that version on my Mac laptop and running it there. Did you use 64 or 32 bit? I won't be able to try this before Monday. On 04/29/2011 11:55 AM, Colin Davey wrote: > 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
