Freesurfer March 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
79 discussions

intergroup t-values
by Cameron Ellis 22 Mar '07

22 Mar '07

Hi all, I am trying to generate a t-map for an intergroup average. when I attempt to run stxgrinder the program looks for a fixed effects average. Since intergroupavg-sess assumes a random effects analysis is it possible to generate this statistic? Is there something statistically repugnant about generating a t-statistic for an intergroup random effects average? Thanks, Cameron

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gray matter misclassified as csf
by Binyam Nardos 21 Mar '07

21 Mar '07

Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

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produce mgz files from ima files of Siemens Scanner
by Thomas Doering 21 Mar '07

21 Mar '07

Hi, i would like to know how i produce the mgz files from dicomfiles with the end ima instead of dcm? Thanks Thomas

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Freesurfer - temporal lobes not included
by deepa preeti 21 Mar '07

21 Mar '07

Hi Bruce, I am trying to do cortical thickness on a few scans. But on many of the subjects after autorecon2, I found temporal regions were not included. When I browsed the archive, it was suggested to add a few control points in the temporal lobe wm, saving the control points and rerunning using the command : recon-all -autorecon2-cp -autorecon3 -subjid subject - which is supposed to do the trick and fix the pial surface as well. Unfortunately, this didn't give me different results when I opened the image using this command : tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white The image was the same, with contol points added, and the temporal regionstillnot included. I have some images for you to look at ( However, I compared the stats ( lh & rh .aparc.2005 and lh & rh aparc ) before adding cp and after adding cp & rerunning eveything --- the values are different. Although the second image still did not include the temporal region, the stats nevertheless gave me different values. I am relatively new to Freesurfer and I appreciate your suggestions and thoughts on this dilemma. Thank you for taking the time to help me with this. Deepa. -- Deepa Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute Department of Neurology Buffalo General Hospital 100 High St. Buffalo, NY 14203 Work: 716-859-7038 Cell: 716-479- 3050 E-Mail: dramasamy(a)bnac.net

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Complex value color scales.
by Greg Appelbaum 21 Mar '07

21 Mar '07

I am trying to display phase information on the cortical surface using tksurfer, but am running into problems with the scale bar. Specifically when plotting scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice looking (continulus) cortical maps, with the correct scale values, but the color bar is showing up inconsistent (two colors). Is there any way to correct this problem, or access the actual color values being projected to the cortical mesh? Greg Appelbaum Post-Doctoral Fellow Center for Cognitive Neuroscience Duke University Box 90999 Durham, NC 27708 Office: (919) 668-3608

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mris_convert second try
by Emily Cooper 20 Mar '07

20 Mar '07

Hi Freesurfer Community, I sent this message to the mailinglist a little bit ago. It never showed up in my mailbox, although it seems to have posted on the mailinglist website. Anyway, on the chance that it didn't mail out properly, I thought I'd resend it, as I still havent been able to figure out what I'm doing wrong. Thanks! Emily ---------- Forwarded message ---------- From: Emily Cooper <ecooper(a)uchicago.edu> Date: Mar 9, 2007 2:27 PM Subject: mris_convert To: freesurfer(a)nmr.mgh.harvard.edu Hi, I have a question about using mris_convert to convert .asc to .mgh. I have a .mgh file I made with mri_vol2surf (target subject as fsaverage). I convert it to .asc using this command: mris_convert -c 010.onerun.space.intval.lh.fsave.mgh /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt.asc then I try to convert it from .asc to .mgh using this command: mris_convert -c lh.010mg2txt.asc /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt2mg.mgh but when I try to load the new .mgh (lh.010mg2txt2mg.mgh) in tksurfer as an overlay: tksurfer fsaverage lh inflated & I get this error: % Loading tal xfm file /home/ecooper/subjects/fsaverage/surf/../mri/transforms/talairach.xfm MRIalloc: could not allocate 443 slices Cannot allocate memory >From the documentation of mris_convert, it seems that lh.010mg2txt2mg.mgh should be identical to the original .mgh (010.onerun.space.intval.lh.fsave.mgh). Is mris_convert unable to convert .asc to .mgh? Or is there something wrong with my commands? Thanks for your time! Emily

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brain size
by roberto toro 20 Mar '07

20 Mar '07

Hello, I would like to measure the size of a bunch of surface reconstructions (ventral-dorsal, posterior-anterior, medial-lateral), but I wouldn't like that the different orientation of the subject's head may affect the measurements (if the head is tilted, for example). Is there a simple way of doing this? ... otherwise, which of the talairach transforms should I use to recover the orientation of the brain (among talairach.xfm, .lta, etc) thank you very much in advance! roberto

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Fw: Problems when testing the bert data
by Thomas Doering 20 Mar '07

20 Mar '07

> Hi, > > i need some little help with the testrun of your nice freesurfer Software > on > my > fedora 2 system, rh9-freesurfer.: > > After installing and setting up i want to try the bert data and it seems > that > there is missing something. libglut.so.3 > > I send you a screenshot of the terminal. > > What can i do? > > Thanks for your help > > regards > > Thomas Doring > Medical Physicist MR > CDPI Rio de Janeiro > > >

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Re: Freesurfer Digest, Vol 37, Issue 15
by Sebastian Moeller 20 Mar '07

20 Mar '07

On 20. Mar 2007, at 15:46 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 8 > Date: Tue, 20 Mar 2007 15:45:25 +0100 > From: Juergen Haenggi <j.haenggi(a)psychologie.uzh.ch> > Subject: [Freesurfer] Error > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <C225B215.CE%j.haenggi(a)psychologie.uzh.ch> > Content-Type: text/plain; charset="US-ASCII" > > Dear Freesurfer users > > I am trying to run Freesurfer on a Mac, but the following error > occured: > > juergen-haenggis-computer:/Applications/freesurfer/subjects > juergenhaenggi$ > tkmedit bert orig.mgz > GLUT: Fatal Error in tkmedit.bin: could not open display: > juergen-haenggis-computer:/Applications/freesurfer/subjects > juergenhaenggi$ > It looks like you did not install and/or start X11, as far as I know (still on 10.3) there should be an additional install for X11 somewhere on the system disk (if it is not installed by default on tiger, then just start X11 before running freesurfer. It might be a good idea to start the freesurfer programs from an xterm otherwise the display error might still persist. Or add the following to you ".bashrc" # so terminal.app can start X11 applications DISPLAY=:0.0 export DISPLAY While not very clean it should do the trick and allow starting of x apps from terminal. ahoi & good luck Sebastian > I use Freesurfer v3.0.5 on Mac OS X Intel Tiger. > > Thanks a lot in advance > Best regards > Juergen > > PS: there was no solution for that problem in the archives > > ----------------------------------------------------------------------- > ---- > Juergen Haenggi, Ph.D. student > Department 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) > j.haenggi(a)psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ----------------------------------------------------------------------- > ---- > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 37, Issue 15 > ****************************************** > > -- 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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higher res recon
by David M Schnyer 20 Mar '07

20 Mar '07

Folks, We have a .7mm cubic voxel SPGR scan we would like to segment with Freesurfer. When I run it with the recon all flag -cm images retain their "native" resolution up to the normalization step of nu to T1. nu.mgz has the native resolution but T1 is converted to 256 cubic. Can I do what I want here? thanks, david -- David Schnyer, Ph.D. Imaging Research Center & Department of Psychology University of Texas, Austin tel: (512) 471-8505 fax: (512) 232-4202 http://irc.utexas.edu/index.html

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Freesurfer March 2007