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
