I just installed Freesurfer. Attached is a tweaked version of your script that runs fine on my MacBook Pro, Intel Core Duo:
[v3:~] donnadierker% caret_command -version Caret Version: 5.616 QT Version: 4.5.4 VTK Version: 5.0.3 Date Compiled: Nov 12 2010 [v3:~] donnadierker% uname -a Darwin v3.wustl.edu 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 I did 'cp -a bert ~/DAVEY' rather than write to the Freesurfer subjects directory. I extracted the PALS_B12.LR.zip into ~/DAVEY as well. And put the script in ~/DAVEY. I don't know if it's the slightly modified directory structure, slightly different Caret version (5.616), or different Macosx version; I just don't know. But it works on my end. > 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 >
preborderBert.sh
Description: Bourne shell script
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