Actually, I didn't see that one!
I'll check my spam folder when I arrive at work, although I don't know why it would treat that one differently from all the other caret-list emails I get. In any case, a belated thanks for that reply, and I'll try what you suggested! _____ From: Donna Dierker [mailto:[email protected]] To: Caret, SureFit, and SuMS software users [mailto:[email protected]] Sent: Fri, 13 May 2011 07:54:03 -0700 Subject: Re: [caret-users] freesurfer pipeline 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
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