Re: [Freesurfer] make_average_surface error?
make_average_subject creates a new subject from its inputs (three in your case). the recon-all -qcache option samples the values from a subject onto the fsaverage subject. so since the fsaverage subject and your uh3 average subject are different surfaces, the vertex numbers wont match. though if you were to sample your uh3 measurements onto fsaverage, then those numbers should match, although not perfectly (the -qcache method is more accurate). n. On Mon, 2010-08-30 at 18:01 -1000, Jeff Sadino wrote: > Hello, > > > I issued this command to make an average subject: > make_average_subject --subjects 2101 2102 2103 --out uh3 > > > I wanted to verify the average thickness file is what it sounds like. > I used the recon-all -qcache on each subject individually, read the > fwhm0 thickness files into matlab, and averaged vertex #100. However, > when I look at vertex #100 from the uh3 surf folder, the numbers don't > match. What is the reason for this? I am using freesurfer 4.3.1. > > > Thank you, > Jeff Sadino > ___ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make_average_surface error?
matlab is 1-based. Look at vertex 101 in matlab. cheers Bruce On Mon, 30 Aug 2010, Jeff Sadino wrote: > Hello, > > I issued this command to make an average subject: > make_average_subject --subjects 2101 2102 2103 --out uh3 > > I wanted to verify the average thickness file is what it sounds like. I > used the recon-all -qcache on each subject individually, read the fwhm0 > thickness files into matlab, and averaged vertex #100. However, when I look > at vertex #100 from the uh3 surf folder, the numbers don't match. What is > the reason for this? I am using freesurfer 4.3.1. > > Thank you, > Jeff Sadino > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] make_average_surface error?
Hello, I issued this command to make an average subject: make_average_subject --subjects 2101 2102 2103 --out uh3 I wanted to verify the average thickness file is what it sounds like. I used the recon-all -qcache on each subject individually, read the fwhm0 thickness files into matlab, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1. Thank you, Jeff Sadino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make_average_surface error
also, what is you SUBJECTS_DIR set to? On Mon, 7 Nov 2005, Doug Greve wrote: Looks like MRISwriteCurvature failed. Can you make sure that average/surf/ exists and is writable, and if there is a lh.avg_sulc there that you have perms to overwrite it? doug Jane Aspell wrote: Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell make_average_surface --subjects jane kader anna make_average_surface input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... 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 jane... The following must be revisited** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_surface error
Looks like MRISwriteCurvature failed. Can you make sure that average/surf/ exists and is writable, and if there is a lh.avg_sulc there that you have perms to overwrite it? doug Jane Aspell wrote: Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell make_average_surface --subjects jane kader anna make_average_surface input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... 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 jane... The following must be revisited** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_surface error
Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell >make_average_surface --subjects jane kader anna make_average_surface input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... 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 jane... The following must be revisited** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
