Thanks - that got it working! I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. Any help is appreciated. Alex
make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 ==================== make_average_surface ==================== input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 output subject: average mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject s1000186... The following must be revisited********************************** Segmentation fault -----Original Message----- From: Itamar Kahn [mailto:[EMAIL PROTECTED] Sent: Tue 6/28/2005 9:51 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_glm The 'make_average_surface' script is in Dos format. You can use the 'dos2unix' application to remove the offending characters from it (dos2unix comes with all linux dist and you can use fink to download it for mac os x). Cheers, Itamar ------------------------- [EMAIL PROTECTED] kahn]$ dos2unix --help dos2unix Copyright (c) 1994-1995 Benjamin Lin Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0) Copyright (c) 1998 Christian Wurll (Version 3.1) Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile outfile ...] -h --help give this help -k --keepdate keep output file date -q --quiet quiet mode, suppress all warnings always on in stdin->stdout mode -V --version display version number -c --convmode conversion mode convmode ASCII, 7bit, ISO, Mac, default to ASCII -l --newline add additional newline in all but Mac convmode -o --oldfile write to old file file ... files to convert in old file mode -n --newfile write to new file infile original file in new file mode outfile output file in new file mode On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote: > Hi Nick, > I copied the script into > the bin dir, but when I type make_average_surface, I get the > following: > > make_average_surface > 'nknown option: `- > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. > > Is this normal? > Thanks, > Alex > > > -----Original Message----- > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > Sent: Tue 6/21/2005 11:00 PM > To: Fornito, Alexander > Cc: Freesurfer Mailing List; Bruce Fischl > Subject: RE: [Freesurfer] mris_glm > Alex, > > Attached is the make_average_surface script. Copy it to the > freesurfer/bin directory, and be sure to make it executable (run > 'chmod > 755 make_average_surface' in the freesurfer/bin directory). > > Type 'make_average_surface' to get help. Basically, just the subject > names are required. By default, a 'subject' named 'average' will be > created from your set of subjects (a name instead of 'average' can be > specified on the command line). > > Nick > > ps. I am working on the mris_surface seg-fault problem using the > rh.orig > file that you sent. > > > On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > >> Hi Alex, >> >> you're better off using the make_average_surfaces.csh script to >> make an >> average of your subjects. Nick: can you send Alex a copy? >> >> thanks, >> Bruce >> On Tue, 21 Jun >> 2005, Fornito, Alexander wrote: >> >> >>> Def. sounds worth doing then! I'll give it a try. >>> My other question is, where can I get my hands on the average7? It's >>> used as the target in the mris_glm examples, but I haven't been >>> able to >>> find the actual average7 surface in any of the freesurfer >>> directories. >>> Am I missing something? >>> Thanks again, >>> Alex >>> >>> -----Original Message----- >>> From: Doug Greve [mailto:[EMAIL PROTECTED] >>> Sent: Tuesday, June 21, 2005 4:11 PM >>> To: Fornito, Alexander >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] mris_glm >>> >>> >>> You can run with just the design matrix, but you won't be able to >>> use >>> the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a >>> way to >>> specify how to build the des mtx. The fsgdf keeps track of what the >>> regressors mean (eg, Age, Class, IQ, etc). When you save the >>> preprocessed data with --y, you'll see that there will be an fsgdf >>> file saved with it. Load this in tksurfer, click on a point, and you >>> will be able to make a scatter plot of, say, thickness vs age, with >>> each class (eg, Male, Female) having a different color dot in the >>> scatter plot. When you mouse-over the dot, it tells you the subject >>> name. Click on a new point and you'll see the scatter plot for that >>> point. If you use --xmat, you can save the design matrix (in >>> matlab-4 >>> format). >>> >>> doug >>> >>> >>> On Tue, 21 Jun 2005, Fornito, Alexander wrote: >>> >>> >>>> Hi, >>>> >>>> I was seeking some clarification re: the relationship between the >>>> >>> fsgdf >>> >>>> and design matrix file for use with mris_glm. It seems to me >>>> that the >>>> two contain very similar info, the examples in the -help don't >>>> use the >>>> fsdf at all. Is it necessary to create one, or can you just run an >>>> analysis with the desmtx? >>>> >>>> Thanks, >>>> >>>> Alex >>>> >>>> >>>> >>>> Alexander Fornito >>>> >>>> M.psych (Clin. Neuro.)/PhD candidate >>>> >>>> Melbourne Neuropsychiatry Centre and Department of Psychology >>>> >>>> The University of Melbourne >>>> >>>> [EMAIL PROTECTED] >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _________________________________________________ Itamar Kahn Department of Psychology Stanford University Jordan Hall, Bldg 420 Mail Code 2130 Stanford, CA 94305 office: 650-724-9515 fax: 650-725-5699 url: http://web.mit.edu/kahn/www _________________________________________________ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
