Any news on this? On Apr 29, 2011, at 1:56 PM, Colin Davey wrote:
> 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
