Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Resuming recon-all
by Martin Ystad 13 Jun '06

13 Jun '06

Hi, some of my subjects crash due to memory-failure way into the recon-all stream. Is there any way I can resume the processing stream from where it crashed without having to write all the individual commands for the rest of the stream? For example, if my subject crashed during autorecon2 -calabel, would there be a command that re-runs -calabel and the rest of the autorecon2 stream? Thanks, Martin Ystad University of Bergen, Norway.

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smoothing
by Lars M. Rimol 13 Jun '06

13 Jun '06

Hi, In the --help output of mri_surf2surf, the following explanation is given for --fwhm-src fwhmsrc: Smooth the source or target with a gaussian with the given fwhm (mm). This is actually an approximation done using iterative nearest neighbor smoothing. The number of iterations is computed based on the white surface. This method is similar to heat kernel smoothing. This will give the same results as --nsmooth-{in,out}, but automatically computes the the number of iterations based on the desired fwhm. What is the equation used to compute the number of iterations, and is it valid for an average surface? -- yours, LMR

3 2

License
by dasoscia＠buffalo.edu 12 Jun '06

12 Jun '06

I'm confused about how to use my license key. It was sent to me, but there isn't a file names .license in my freesurfer home folder. And there isn't a license key FILE, only the three lines of text sent to me. What should I type in the command line to validate the license?

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mri_convert problem
by dasoscia＠buffalo.edu 12 Jun '06

12 Jun '06

I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I change the directory to /subjects, then I type the following with the error: [amc@amcpacs subjects]$ recon-all -i 1593-4/Image0001.dcm -s 1593-4 ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ WM removal version $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag -i unrecognized. -i 1593-4/Image0001.dcm -s 1593-4 I dont know why it doesnt recognize the -i flag...but this is repeatedly the wall I am running into. Any ideas? Dave

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Re: Freesurfer Digest, Vol 28, Issue 15
by Sebastian Moeller 11 Jun '06

11 Jun '06

Hi All, On 11. Jun 2006, at 19:09 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 3 > Date: Fri, 9 Jun 2006 15:19:42 -0400 > From: "Gifford, Sheyna" <Sheyna_Gifford(a)brown.edu> > Subject: [Freesurfer] freesurfer on windows thru ssh > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <26B871D42497A946A1F25421794CEE8A0382C9A7(a)MAIL1.AD.Brown.Edu> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Freesurfer Community, > > Freesurfer is running well on Mac OSX and BSD, but one of my users > wants to run it on Windows thru ssh. This is the error that is > generated when she tries. > >> GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by >> display: localhost:14. > > I am not at all a windows person. I can only imagine that this has to > do with lack of OpenGL support on WindowsXP. > > Has anyone out there in the community successfully been able to run > freesurfer on Windows, thru eXceed or any other method? If you have root at the linux machine try to install freenx. Combined with nomachine's (www.nomachine.it) client software freesurfer remote controlling works down to adsl speeds, where X11 over ssh long lost its usability. Ahoi Sebastian > > Many thanks for any advice. > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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center of pial surface in world coordinates
by martijn van den heuvel 11 Jun '06

11 Jun '06

Dear Bruce, Thanks for your quick reply. I posted this question on the Neurolens-forum as well. I too think it is just a problem of two different coordinate system. Rick (of the Neurolens forum) mentioned that the pial surface coordinate to world coordinate system is stated in a COR.info file. However, I think that the COR.info file is no longer supported by freesurfer, is this correct? Is there an alternative? Sorry, if my question was not totally clear. I will describe what I did: I translated my anatomy file to talairach space (only translation, no scaling, resliced it so there is not .mat file ) and used it (in SPM analyse format) as input for the freesurfer-train (recon-all -autorecon1,2,3). The recon-all dev table suggests that freesurfer uses brain.finalsurfs.mgz (same orientation as T1.mgz) as the input for creating the surface pial files. In my original anatomy file the (0,0,0) coordinate is around the center of the brain (in talairach space). As my input anatomy is already in Talairach space orig.mgz is also in talairach space and there is a minimum translation by freesurfer to create T1.mgz (I checked this and indead talairach.xfm is almost a 1 1 1 matrix). If freesurfer uses this as the input for the surface rendering, should not be the (0,0,0) coordinate in the middle of the pial surface? Using tksurfer this is indead the case, however using Neurolens this is not the case, there is a large shift. There is a small shift from talairach coordinate system to RAS system, but my surface rendering has a much larger shift (in my example around 45 mm in the Z-direction). Maybe this COR.info file is the solution, holding the translation from scanner coordinates <-> RAS, however I don't have an example of this file and therefore do not now what this file looks like and what it does. Hope you can help me with this problem. Really appreciate your time. greetings, martijn > > > > > > On 6/7/06, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > wrote: > > >> > > >> I think it's probably just displaying them in different coordinate > > >> systems. tksurfer displays in an RAS coordinate system in which > > (0,0,0) > > >> is essentially the center of the volume, whereas Neurolens is > > probably > > >> displaying scanner coordinates. Does it matter to you? Not sure I > > >> understand - is it causing you any problems? > > >> > > >> Bruce > > >> > > >> On Wed, 7 Jun 2006, martijn van den heuvel > > >> wrote: > > >> > > >> > Dear freesurfer-users, > > >> > > > >> > I want to plot the freesurfer surface rendering (xxx.pial) in the > > >> program > > >> > Neurolens. Loading the image gives no problem and Neurolens gives a > > > > >> > beautiful rendering. However, when loading the pial surface in > > tksurfer > > >> I > > >> > see a difference between the two renderings. The surface in > > tksurfer is > > >> > centered to RAS (0,0,0) , like the T1.mgz image (as it supposed to > > do). > > >> Im > > >> > trying to figure out what this translation is, but I cannot find > > the > > >> answer > > >> > on the web, hence this email. Does tksurfer loads in a translation > > file > > >> > (except for the talaraich.xfm, I got this translation covered), or > > does > > >> it > > >> > do a general shift to the RAS centre? Generally, Im looking for the > > >> > translation matrix from RAS to world coordinates, so I can apply > > this > > >> > translation to the surface before loading it in Neurolens. > > >> > > > >> > I hope someone can help me with this question. > > >> > > > >> > Yours sincerely, > > >> > > > >> > Martijn van den Heuvel > > >> > > > >> > > > > > > >

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freesurfer on windows thru ssh
by Gifford, Sheyna 09 Jun '06

09 Jun '06

Dear Freesurfer Community, Freesurfer is running well on Mac OSX and BSD, but one of my users wants to run it on Windows thru ssh. This is the error that is generated when she tries. >GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by >display: localhost:14. I am not at all a windows person. I can only imagine that this has to do with lack of OpenGL support on WindowsXP. Has anyone out there in the community successfully been able to run freesurfer on Windows, thru eXceed or any other method? Many thanks for any advice.

2 1

SPM conversion to FreeSurfer-style reg matrix
by jswonder 09 Jun '06

09 Jun '06

Hello all, I am looking for a way to convert an SPM .mat to a FreeSurfer registration matrix (register.dat); basically, something like the old spmmat2register command, but not obsolete...any suggestions? Thanks!

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Re: group analysis error
by adam walczak 09 Jun '06

09 Jun '06

never mind...figured out. thx --- adam walczak <xfadam(a)yahoo.com> wrote: > Hello, > > While running group analysis (mri_glmfit step), on > an > admittedly tiny subject group (3). I used two > classes > (male/female) and age. I received the following > error: > > ERROR: DOF = 0 > > I am wondering if three subjects is too small a data > set for this to run or if I am just doing something > wrong. It got through the other preprocessing > steps, > but got stuck here. > > My contrast vector is [0 0 1] like the tutorial. > > Thanks for any help. > > Adam > > adam > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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group analysis error
by adam walczak 09 Jun '06

09 Jun '06

Hello, While running group analysis (mri_glmfit step), on an admittedly tiny subject group (3). I used two classes (male/female) and age. I received the following error: ERROR: DOF = 0 I am wondering if three subjects is too small a data set for this to run or if I am just doing something wrong. It got through the other preprocessing steps, but got stuck here. My contrast vector is [0 0 1] like the tutorial. Thanks for any help. Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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