RE: [Freesurfer] TkmEdit message
Have you installed the X11Update2006 package from Apple? I think that fixes this problem. A copy of it is here: http://surfer.nmr.mgh.harvard.edu/pub/dist/X11Update2006.dmg http://surfer.nmr.mgh.harvard.edu/pub/dist/X11Update2006.dmg Which OS are you using? From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anil Roy Sent: quinta-feira, 4 de outubro de 2007 22:17 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TkmEdit message Hi, When I run tkmedit, I receive the following message. It doesn't seem to affect the functionality. Could you explain why this message shows up. Xlib: extension XFree86-DRI missing on display : 0.0. Thanks, Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] help on installation under VMWARE + suse 10.2
I'm not sure VMWare is full OpenGL compliant, other options are Qemu or Xen, this last one has a better performance. Maybe you should try to use an exclusive Linux machine. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Xue,Gui Sent: quinta-feira, 4 de outubro de 2007 16:22 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] help on installation under VMWARE + suse 10.2 hi-I am trying to install freesurfer my computer with the following settings: Operating system: Win XP Open Suse10.2 running under vmware workstation 6.0. Display card: NVIDIA Quadro FX 3400/4400. The problem I have is that the tksurfer doesn't work well, like what's described on the wiki, only small part of the surfer was shown. I updated the display card driver, but it didn't fix the problem. I wonder if anyone has successfully configure the system to make it work. Thanks a lot! gui ___ 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
[Freesurfer] multiple surface overlays
Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer subject hemi surface -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] multiple surface overlays
Yes, you can do it with scripting. Start by checking out this page: http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting_2fTkSurferIntroToScripting In your case, if your overlay files are volumes, you should use the function sclv_read_from_volume instead of sclv_read_from_dotw. Reference for scripting commands is here: http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting_2fTkSurferScriptingReference On Fri, 2007-10-05 at 13:52 -0400, Cameron Ellis wrote: Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer subject hemi surface -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg-sess error
Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -- ??? Error using == minus Matrix dimensions must agree. Error in == fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); ??? Undefined function or variable 'r'. quiting matlab -- ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selxavg-sess error
This should be fixed in both dev and stable on the next update [EMAIL PROTECTED] wrote: Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -- ??? Error using == minus Matrix dimensions must agree. Error in == fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); ??? Undefined function or variable 'r'. quiting matlab -- ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] model for pair-T test
Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TkmEdit message
I'm using Red Hat Linux release 9. Does this update apply to linux users also? Thanks, Anil. On 10/5/07, Pedro Paulo Oliveira Jr [EMAIL PROTECTED] wrote: Have you installed the X11Update2006 package from Apple? I think that fixes this problem. A copy of it is here: http://surfer.nmr.mgh.harvard.edu/pub/dist/X11Update2006.dmg Which OS are you using? *From:* [EMAIL PROTECTED] [mailto: [EMAIL PROTECTED] *On Behalf Of *Anil Roy *Sent:* quinta-feira, 4 de outubro de 2007 22:17 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] TkmEdit message Hi, When I run tkmedit, I receive the following message. It doesn't seem to affect the functionality. Could you explain why this message shows up. Xlib: extension XFree86-DRI missing on display : 0.0. Thanks, Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
