I assume you saw this, which is more recent than the post below: http://www.mail-archive.com/[email protected]/msg02319.html
I have not done anything since then, as multiple projects demand my time right now. The one I would do if I did have the time is upgrade Caret versions. Have you tried running it with a directory structure more like what I used? I'm not clear on why it would matter, but I lack the knowledge/skills to debug in MacOSX. On 05/12/2011 12:20 PM, Colin Davey wrote: > 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
