[Freesurfer] fs-fast smoothing
Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fs-fast smoothing
Thanks Doug, though I'm still a bit confused: I'd like to see the smoothed results on the individuals, not just the group - so it seems isxconcat-sess wouldn't be appropriate. Are you suggesting running mri_surf2surf directly on the contrast sig.nii files? Is smoothing a significance map the equivalent of smoothing the data, then recreating the significance in the sphere space? This didn't seem true to me, which is why I tried to recreate the significance maps as below. Thanks, -S Doug Greve wrote: Hi Scott, you should skip steps 2-6 (that is the old stream). Instead, run isxconcat-sess after #1, then smooth on the surface either in isxconcat-sess or with mri_surf2surf before running mri_glmfit. doug Scott Gorlin wrote: Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott ___ 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
Re: [Freesurfer] fs-fast smoothing
no, i'm using 4.1 stable. is the development version open to the public? (i don't see anything here: http://surfer.nmr.mgh.harvard.edu/pub/dist/dev-releases/) Or a patch/some minor edits I can copy into preproc-sess? Or a *not the easiest* way :)? thanks again Doug Greve wrote: Oh, in that case the easiest thing to do is to smooth the raw data on the surface. If you have a development version of freesurfer, you can do this with preproc-sess using the -surf-fwhm option doug Scott Gorlin wrote: Thanks Doug, though I'm still a bit confused: I'd like to see the smoothed results on the individuals, not just the group - so it seems isxconcat-sess wouldn't be appropriate. Are you suggesting running mri_surf2surf directly on the contrast sig.nii files? Is smoothing a significance map the equivalent of smoothing the data, then recreating the significance in the sphere space? This didn't seem true to me, which is why I tried to recreate the significance maps as below. Thanks, -S Doug Greve wrote: Hi Scott, you should skip steps 2-6 (that is the old stream). Instead, run isxconcat-sess after #1, then smooth on the surface either in isxconcat-sess or with mri_surf2surf before running mri_glmfit. doug Scott Gorlin wrote: Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott ___ 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] tksurfer overlay scale bar label colors
Hi, When I display an overlay scale bar in tksurfer, the labels for the scale bar are displayed in black on a black background. Obviously, this is completely unusable since I cannot read them! They are there, however, because if I move the surface over so that it underlies the scale bar, the text shows up (in black) just fine. Some time ago the text was rendering in blue, which I thought was an odd choice but gave no further thought to it until I noticed the text disappear completely. Now, it seems like a bug to me, but unfortunately I did not notice exactly when the switched occurred. Unless there is some setting buried somewhere to control the text color? I'd love to just set it to white and not deal with this again... I have upgraded both my os and my graphics drivers recently so I wonder if that broke something. The only clue I have is that I know the newest ATI drivers run on AIGLX instead of XGL, could that cause any errors? I'm seeing this in both FS 3 and 4: tksurfer --all-info on my v.4 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2008/03/03-22:12:05-GMT BuildTimeStamp: Sep 17 2007 17:25:01 CVS: $Id: tksurfer.c,v 1.276.2.5 2007/09/16 23:37:27 greve Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 tksurfer --all-info on my v.3 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 08/03/03-22:14:40-GMT CVS: $Id: tksurfer.c,v 1.183.2.11 2007/01/04 22:30:38 nicks Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 My system: Ubuntu 7.10 (recently upgraded from 7.04) pentium 4 fglrxinfo returns: display: :0.0 screen: 0 OpenGL vendor string: ATI Technologies Inc. OpenGL renderer string: RADEON X600 Series OpenGL version string: 2.1.7281 Release glxinfo | grep direct returns: direct rendering: Yes xdpyinfo | grep GL returns: ATIFGLEXTENSION ATIFGLRXDRI GLX SGI-GLX Thanks a lot, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
i just fixed something like this on ubuntu 7.10 with an ati radeon x600. the latest drivers run on aiglx which conflicts with the previous versions which run on xgl. this sometimes even caused X to crash when running tksurfer and even glxgears. on my system this was resolved by simply removing the package xserver-xgl. there should be no reason to uninstall the proprietary fglrx driver. Goradia, Dhruman D wrote: Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen ___ 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 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
Re: [Freesurfer] Black digits and black background
i had the same problem on ubuntu after i upgraded to the latest drivers on my ati video card. i could only get proper white labels by switching to an older driver, which wasn't a good solution for other reasons. i switched to an nvidia card and this resolved the issue. Juergen Haenggi wrote: Dear FS experts When loading a thickness map in FS 4.0.3 for MacOS X Leopard the thickness values of the colour scale bar are not visible because they are printed in black like the background. How can I change the colour of these mm values from black to white? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) --- ___ 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] fsfast file question
Hi, I have a question about files produced by fsfast selxavg3-sess. After a successful run, I see that it produces contrast folders in the appropriate analysis folder inside of /bold/, but there is also a folder named res which is quite large (including a file 'all.nii' which, in my case, is over 1 gb). I don't see this folder described anywhere in the fsfast documentation. I presume these are the residuals after the glm analysis? Are they necessary for any other fsfast/freesurfer commands, or are they safe to delete if i don't need to examine the residuals? Thanks, Scott ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
