Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

Difficulties with segmentation follow-up
by Jeffrey Spielberg 11 May '07

11 May '07

Hi, I sent a message to the forum last June regarding a problem with segmentation of the acc we were running into. We kept having areas of the rostral and caudal acc labeled as corpus callosum or "unlabelled subcortical". I got a reply that this was being worked on and I was wondering if this is now fixed in 3.0.4, and if not if there is any timeline for releasing a fix? Thanks, Jeff

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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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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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cluster-wise analysis of functional overlap...
by Mark Fenske 30 Jan '07

30 Jan '07

Hi there, I am comparing regions of activation from two different sets of functional data, and would like to make a statement about the likelihood that the area of overlap (i.e., the common area of significant activation for both contrasts) is due to chance (or, more precisely, my confidence that it is not due to chance). It seems to me that an extension of the Monte Carlo approach used with mri_glmfit to correct for multiple comparisons might work well for this, so I'm wondering whether this might be possible with the current set of freesurfer/fs-fast tools. Specifically, I'd like to: - use mri_glmfit to twice run the Monte Carlo simulator (mc-full-- input noise, smooth, and analyze) for each of n-thousand iterations. - submit the two resulting activation maps to something like mergecontrasts-sess to obtain a map of the clusters of overlapping activation (-conjunction and) - use these clusters-of-overlap to provide cluster simulation data (CSD) to mri_surfcluster along with my original map of clusters of overlapping activation in order to calculate the corresponding cluster-wise p-values (CWP). If my reasoning is correct, the CWP values following this procedure would be indicative of the probability associated with areas of overlapping activation, rather than the likelihood of obtaining a cluster of certain size/significance, per se. The main outstanding questions before doing this seem to concern: - getting the output of each of the two Monte Carlo simulations so that extent of overlap in the different sets of clusters can be computed -- Is there a way to pipe the simulation output to a glmdir? - computing the areas of overlap for clusters from each pair of simulations. It's not clear to me how to feed these two maps as input to mergecontrasts-sess. -- Is there a way to provide direct paths for the inputs to mergecontrasts, rather than rely on the -analysis, -contrast etc. flags? - assessing the list of clusters resulting from mergecontrasts-sess in order to get a CSD file that can be fed into mri_surfcluster Any comments on this approach, and especially suggestions to help in its implementation would be greatly appreciated. Thanks, Mark ----- Mark J. Fenske, Ph.D. MGH Martinos Center for Biomedical Imaging - Harvard Medical School Tel: (617) 726-9034 | Fax: 726-7422 | http:// barlab.mgh.harvard.edu/fenske.htm

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surf2surf
by Chacko Cherian 30 Jan '07

30 Jan '07

Hello users, I wanted to use mri_surf2surf for surface smoothing but it gives me an error saying --s is not an option. mri_surf2surf --hemi lh \ --s average \ --sval lh.gender_age.thickness.mgh \ --fwhm 10 \ --tval lh.gender_age.thickness.10.mgh it didnt work with srcsubject either.The average subject is in the $SUBJECTS_DIR. 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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glibc detected
by Nurunisa Neyzi 30 Jan '07

30 Jan '07

Hi, when I try to redo the parcellation with another gcs file, and type the command: mris_ca_label 2560_4 lh lh.sphere.reg gcs_jan07/lh.outputclassifier.gcs lh.renewparc.annot I get the following error/log: $Id: mris_ca_label.c,v 1.16 2006/02/14 20:25:59 nicks Exp $ $Id: mrisurf.c,v 1.441 2006/02/24 20:40:56 fischl Exp $ reading atlas from gcs_jan07/lh.outputclassifier2.gcs... INFO: NOT fixing vertex area *** glibc detected *** free(): invalid pointer: 0x0000000000943580 *** Aborted I am not sure what is going wrong and would appreciate some guidance.

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Freesurfer January 2007