Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Variability and randomness in algorithms
by Bo Shi 02 Feb '07

02 Feb '07

Hi, Sorry to dredge up an old thread, I was curious about the details on where randomness is introduced in the following programs (beyond the normal floating points issues): > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234 I assume that the Segonne, Grimson, and Fischl paper on the genetic algorithm for cortical surface correction applies to mris_fix_topology? Is it also the case that the randomness is injected in other min/maximization-type algorithms in the other functions? > RE: [Freesurfer] variability > Nick Schmansky > Thu, 21 Dec 2006 10:14:12 -0800 > > Valentina, > > The randomization in the algorithms accounts for about a 0.02% change > in thickness results. You can disable randomness (or rather, force > seeding the rng with same number) by including the flag -norandomness > with recon-all. This flag is available in v3.0.4. > > In older versions, do this to disable randomness: create a file called > xopts containing this text: > > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234

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mri_convert orientation
by Fornito, Alexander 01 Feb '07

01 Feb '07

Hi, I'm trying to convert a series of siemens dicom mosaic format files to analyze format, while reorienting at the same time. Running the command below converts and reorients only the filename specified in the command line (which is the first file in the series), whereas leaving out the --out_orientation flag converts all the files in the series. Is it only possible to convert AND reorient one file at a time? Or is there something I'm missing that would allow me to convert and reorient all the files in the series with a single command? Thanks, Alex mri_convert -it siemens_dicom 93663320 -ot analyze test_ --out_orientation LPS Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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Re: bad surfaces?
by Glenn Lawyer 01 Feb '07

01 Feb '07

Hi, I'm wondering if I missed something between the 3.0.3 and 3.0.4 release. Does the latest version constrain medial pial surfaces across hemis? There was a question on this on 5 may 2006, (quoted below) and at that time there was no constraint. > no, they aren't constrained across hemis, although of course they should be. > --Bruce > On Fri, 5 May 2006, Josh Snyder wrote: >> I see this on a ton of datasets. Is it a known issue? Is there an easy >> correction? Thanks,Josh freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 3 > Date: Wed, 31 Jan 2007 12:16:19 -0600 (CST) > From: Derin Cobia <derin(a)conte.wustl.edu> > Subject: [Freesurfer] Bad surfaces? > > I reran our subjects from "final_surfaces" on through autorecon3 using > 3.0.4 to correct for the pial surface crossover at the midline (as > recommended by Bruce). > -Derin > > > > ****************************************** > -- -------------------------------------- I'm only in it for the glory . + Glenn Lawyer + + +352 661 967 244 + + Instituttgruppe for psykiatri + + Postboks 1130 Blindern + + 0318 Oslo + + http://folk.uio.no/davidgl + +++++++++++++++++++++++++++++++++++:)

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tkmedit/tksurfer fail at startup with X BadValue errors
by Graham Wideman 31 Jan '07

31 Jan '07

Folks: On an installation that had been working, suddenly we're getting fatal errors on starting either tkmedit or tksurfer. These appear to be errors trying to perform X functions. Command lines and responses shown below. I am not aware of recent changes to the environment (new software installed etc) that would relate to this... but one never knows. 1. Anyone happen to know exactly what solves this? 2. Any clues as to how to troubleshoot would be helpful (eg: is there a log that these programs write into at this early of a stage in startup?) Thanks, Graham ================= Initialization ================= [graham@gwlinux ~]$ tcsh [graham@gwlinux ~]$ source /brain-bin/fs_20060528/centos4/freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer FSFAST_HOME /brain-bin/fs_20060528/centos4/freesurfer/fsfast SUBJECTS_DIR /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline FUNCTIONALS_DIR /brain-bin/fs_20060528/centos4/freesurfer/sessions MINC_BIN_DIR /brain-bin/fs_20060528/centos4/freesurfer/mni/bin MINC_LIB_DIR /brain-bin/fs_20060528/centos4/freesurfer/mni/lib PERL5LIB /brain-bin/fs_20060528/centos4/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /brain-bin/fs_20060528/centos4/freesurfer/lib/tcltktixblt/lib FSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/fsl ================= tkmedit: ================= [graham@gwlinux ~]$ which tkmedit /brain-bin/fs_20060528/centos4/freesurfer/bin//tkmedit [graham@gwlinux ~]$ tkmedit X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 78 (X_CreateColormap) Value in failed request: 0x0 Serial number of failed request: 15 Current serial number in output stream: 17 [graham@gwlinux ~]$ ================= tksurfer ================= [graham@gwlinux bxbaseline]$ tksurfer 85432 rh white surfer: current subjects dir: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: Reading header info from /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline/85432/mri/T1.mgz surfer: vertices=184105, faces=368206 surfer: single buffered window Received X error! Error code : 2 Request code : 78 Minor code : 0 Error text : 'BadValue (integer parameter out of range for operation)' Received X error! Error code : 12 Request code : 1 Minor code : 0 Error text : 'BadColor (invalid Colormap parameter)'

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my_average and fsaverage
by Chacko Cherian 31 Jan '07

31 Jan '07

Hello users, I created an average subject(my_average) with 25 subjects.Now when I compare the fsaverage and my_average inflated views,the display shows fsaverage as way bigger than my_average.Is this normal?Is it something to do with how fsaverage is scaled and displayed? Area-wise my_average is greater than fsaverage. Thanks in advance, Chacko. ____________________________________________________________________________________ Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather

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TIV in group analysis
by Chacko Cherian 31 Jan '07

31 Jan '07

Hello all, Is calculation of TIV taken into consideration while performing the group analysis? Thanks Chacko ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front

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About the FDR button
by jorge luis 31 Jan '07

31 Jan '07

Hello all I am using the genome interface to XWindows in Linux Centos 4 X86-64. I have a problem with the freesurfer interface for FDR correction in tksurfer. The "Configure Overlay Display" window is to large for the screen and the FDR button is hide down. I have proved to change the display resolution but I am still unable to press this button. If you don't know how to solve this problem, please, let me know at least how to call the FDR function from the command line. Thank you so much. Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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Bad surfaces?
by Derin Cobia 31 Jan '07

31 Jan '07

I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks. -Derin

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Freesurfer and Grid computing
by Andries van der Leij 31 Jan '07

31 Jan '07

________________________________ From: Andries van der Leij Sent: Wednesday, December 06, 2006 5:59 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Freesurfer and Grid computing Dear Freesurfer community, I'm a PHD student at the university of Amsterdam and I'm currently investigating the possibilities to streamline our MRI data processing stream. Next summer we'll obtain a research-only scanner. I'm trying to push the group to also invest in computing power and am currently investigating the applications that researchers will most probably use. I came across a project of the group of Cohen at UCLA. They have configured a Apple (unix) grid and have proposed a more or less standard setup specially designed for MRI analyses: http://airto.bmap.ucla.edu/mt-static/NICluster/archives/2005/06/welcome. html It is my understanding that one of the members has rewritten the FSL code which allow distributed parallel processing in a Grid. See the benchmarks here: http://airto.bmap.ucla.edu/bmcweb/bmc_bios/MarkCohen/Apple/Benchmarks.ht m My question is fairly simple: Are similar steps taken in the Freesurfer community? I have no experience with this app myself, but it is my understanding that Freesurfer consumes a lot of resources. Thank you very much in advance, Andries van der Leij

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Hi,I met a problem!
by zhang yi 31 Jan '07

31 Jan '07

Hi, After I open the lh inflated surface, I want to open another pial surface according to the freesurfer tutorial. But, the computer showed that "core dumped" "alloc: invalid block 0xb65d20: 0 0 75" I tried many times, it showed the same above notes every time. So, I don't known what's with it. My computer hardware, memory or something else? I appreciate your help! zhang yi zhang yi 2007-01-31

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