64 bit, thanks! I don't know if this helps, but it's Caret v5.62, and OSX 10.6.6.
On Apr 29, 2011, at 1:19 PM, Donna Dierker wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
