Any news on this? :) On May 3, 2011, at 1:11 PM, Colin Davey wrote:
> Thanks! > > It might just take copying the data that was processed up until that point > from your Linux machine to your Mac, and then trying that one Caret command. > > If replicates the problem, then you're ready to troubleshoot. Of course if it > doesn't replicate it, then the problem could be traced to the earlier > processing, and would need the Freesurfer installation. > > On May 3, 2011, at 11:15 AM, Donna Dierker wrote: > >> Not yet. I thought I could avoid installing Freesurfer, just copy over >> bert, but then I realized the script uses Freesurfer executables. >> >> And I have a slew of other stuff going on. Haven't forgotten. Hope to >> get to it tomorrow. >> >> On 05/03/2011 12:54 PM, Colin Davey wrote: >>> 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 >>> >> >> _______________________________________________ >> 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
