Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Subgenual problems
by Alex Fornito 16 Sep '07

16 Sep '07

Hi all, I've been having problems getting accurate surfaces in the subgenual cingulate region, as illustrated in the attached pics. I previously posted to the list about this, and you sent me a newer mris_surf for an older version of freesurfer that fixed the problem in some, but not all cases. It seems like the new version (included with 4.0) is still giving me some grief. Any suggestions re: what I can do? Thanks for your help, Alex (I'm re-posting this query as per Bruce's request last week.) Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au www.psychiatry.unimelb.edu.au/mnc

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cluster/peak vertex infomation
by Catherine Alexandra Hartley 16 Sep '07

16 Sep '07

Hi, I have a few questions, the answers to which probably all involve running mri_surfcluster with the correct arguments specified. 1) What is the easiest way to obtain peak vertex information from a given cluster? 2) For a given sig.mgh file, is there a command which outputs a list/text file of all clusters present? 3) Is there a way to restrict the clusters displayed in the sig.mgh file to clusters of a given # of vertices or larger? Thanks in advance for your help! -Cate

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mri_convert problem?
by Jessica Andrews-Hanna 16 Sep '07

16 Sep '07

Hi - Does anyone know if there is a problem with mri_convert used within the context of unpacksdcmdir? When I type the following at the command line (which we've used several times successfully in the past in the Buckner lab): ssh nexlin6 source /space/freesurfer/nmr-std-env cd /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts unpacksdcmdir -src `/usr/pubsw/bin/findsession 070814_4TT00316 | grep PATH | awk '{print $3}'` -targ ../ -cfg 070814_4TT00316_unpack_fsl.cfg -unpackerr I get the following error: mri_convert /space/archive/133/siemens/ TrioTim-35006-20070814-165946-670000/670000-3-1.dcm ..//anat/ 003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii -- nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation Here's some useful information using bugr: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: nexlin6 SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts Thanks very much, Jessica

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OpenGL, GLX, X11, VNC with FreeSurfer
by Troy Mcan 15 Sep '07

15 Sep '07

Hi All, I'm trying to connect to a computer remotely to use freesurfer. However, when I log in and try to load up a surface in freesurfer, I get the following message: -No glx extension! -Surfer: failed, trying double buffered window -Xlib: extension "GLX" missing on display "computer name" -Window type not found! -Surfer: failed, no suitable display found I am using a VNC viewer (from www.realvnc.com) to log into the computer. Are there any software rendering solutions for freesurfer so the VNC doesn't run into the openGL problems? Or, on the other hand, are there any VNC clients that are known to work with freesurfer? Thank you very much! _________________________________________________________________ Gear up for Halo® 3 with free downloads and an exclusive offer. It’s our way of saying thanks for using Windows Live™. http://gethalo3gear.com?ocid=SeptemberWLHalo3_WLHMTxt_2

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(no subject)
by Jessica Andrews-Hanna 14 Sep '07

14 Sep '07

Hi Doug - Does anyone know if there is an issue with mri_convert or unpacksdcmdir? I ran mri_convert within unpacksdcmdir. Here is what was typed at the command prompt: unpacksdcmdir -src `/usr/pubsw/bin/findsession $subjName | grep PATH | awk '{print $3}'` -targ ../ -cfg "$subjName"_unpack_fsl.cfg -unpackerr The error I get is: mri_convert /space/archive/133/siemens/ TrioTim-35006-20070814-165946-670000/670000-3-1.dcm ..//anat/ 003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii -- nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation We've used this line plenty of times with success in the past in the Buckner lab. Here's some useful information using bugr: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: nexlin6 SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts --------------------------------------------------------------------- Thanks, Jessica

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using tkmedit
by Robert Levy 14 Sep '07

14 Sep '07

Hi, I am attempting to work with volume data for the first time and trying to figure out how to control what temporal offset is shown in the functional overlay. I checked the options, the wiki, etc, but didn't find anything yet. That is most like because I'm looking at old data that was generated in a way that is incompatible (it seems) with newer versions, so I am sourcing stable2. The command that originally generated the group comparison I am viewing is intergroupavg-sess -analysis EMerror -contrast ASevASc -group1 BwGroupNormalsError5 -group2 BwGroupAspError5 -intergroup BwGroupError5 -space tal -spacedir tal This is the path to the resulting group comparison /space/balagula/8/users/EMexec/fMRI/GROUP_ANALYSIS/BwGroupError5/bold/EMerror/tal-rfx/ASevASc/ To view it I am running: tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map minsig -s BwGroupError5 -isxavg random -fthresh 1.3 My environment looks like: FREESURFER_HOME /usr/local/freesurfer/stable2 FSFAST_HOME /usr/local/freesurfer/stable2/fsfast SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR FUNCTIONALS_DIR /usr/local/freesurfer/stable2/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 GSL_DIR /usr/pubsw/packages/gsl/current QTDIR /usr/pubsw/packages/qt/current TCLLIBPATH /usr/local/freesurfer/stable2/lib/tcltktixblt/lib FSL_DIR /usr/pubsw/packages/fsl/current Thanks for any advice, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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QDEC question
by Narly A Golestani 14 Sep '07

14 Sep '07

Dear all, I have 2 questions regarding doing analyses using QDEC: 1) can I use QDEC to analyse results on data for which I ran recon-all using the last (ie: older, not most recent) version of Freesurfer, or should I rerun recon-all on all the data using the new version of Freesurfer? (I hope not the latter!) 2) I have run the preprocessing required for using QDEC (ie, recon-all -s <subjid> -qcache) on one subject for whom I had run recon-all using the previous version of Freesurfer, and I get the following error messages: WARNING: File rh.volume does not exist skipping creation of smoothed data for rh.volume WARNING: File rh.white.K does not exist skipping creation of smoothed data for rh.white.K WARNING: File rh.white.H does not exist skipping creation of smoothed data for rh.white.H WARNING: File rh.jacobian_white does not exist skipping creation of smoothed data for rh.jacobian_white what might this mean? thanks in advance, best, Narly.

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High Resolution Standard Brain
by Dick, Rachel 14 Sep '07

14 Sep '07

Hello, I have T1 images at 0.8 x 0.8 x 0.8...Is there a high resolution (0.5-0.8) standard brain that I can co-register my images to in place of Freesurfer's? Also, does anyone know of a standard child/adolescent brain that is in use? Thanks in advance, Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry & Behavioral Neuroscience WSU Medical School brain.wayne.edu <mailto:rcondon@med.wayne.edu> (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.

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RV: Re: [Freesurfer] Spherical ROIs areas in the fsaverage
by jorge luis 14 Sep '07

14 Sep '07

Ok, but my automatic procedure constructed the ROI masks on the lh.sphere (not on lh.sphere.reg)of the fsaverage subject. Is it wrong to compute the area of a ROI in the fsaverage spherical surface by adding the areas of the triangular faces inside this region? (The area of each triangular face being computed using the spherical coordinates of its vertices and the Heron formula for the triangle area) Thank you for your useful help Jorge ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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question re: p-vals and t-vals in FreeSurfer
by d.g.lawyer＠medisin.uio.no 14 Sep '07

14 Sep '07

Hi, I'm seeing some odd behavior in t-values and p-values exported from FreeSurfer. In geeky detail: fit a linear model using FreeSurfer, saving t and p-values convert output files to ascii load ascii files into R convert the FreeSurfer "p-values" into real p-values via lh.pval <- 10^(-1*abs(freesurfer.lh.pvals)) # this is necessary as FreeSurfer writes the -log10 of the pvalue, with the sign # demonstrating direction of effect. convert these pvalues to tvalues lh.convert.t <- qt(lh.pval,XX) # where XX is the degrees freedom # I have several studies, 60 < XX < 200 A histogram of lh.convert.t is roughly OK, could be zero-mean. HOWEVER, the t-values exported by FreeSurfer are not. In one study, the range of the converted t-values was [-3.8, 3], but the range of the raw t-values was [-0.6,3.8]. In a second study, the range of the raw t-values was [0,17]. As you could guess from these ranges, histograms of the two versions of t-values also differ radically. Regarding version numbers and such, I have three experiments I have checked for this phenomenon. Two are old, and were run using version 1.2 (output files in .w format, etc), and the third study is new (version 3.X, outputs are F.mgz and sig.mgz). We run the linux/RHEL versions. My questions: why are the t-values output by FreeSurfer so oddly distributed? and why don't they agree with what i get when I convert the p's to t's? Silly user error on my part? Thanks much for any insights

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Freesurfer