Freesurfer

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30080 discussions

segmentation fault error, mri_ca_register
by Teddy Youn 31 Mar '08

31 Mar '08

Hi all, I have a scan of a patient that I've tried troubleshooting via the listserv and fswiki, but with no success. Generally, during mri_ca_register, I end up with a segmentation fault of the following: ----------------- gca peak Unknown = 0.94091 ( 0) gca peak Left_Inf_Lat_Vent = 0.14709 (39) gca peak CSF = 0.14344 (47) gca peak Left_Accumbens_area = 0.20088 (67) gca peak Left_undetermined = 0.98433 (34) gca peak Left_vessel = 0.32698 (60) gca peak Left_choroid_plexus = 0.11007 (56) gca peak Right_Inf_Lat_Vent = 0.20176 (34) gca peak Right_Accumbens_area = 0.32293 (69) gca peak Right_vessel = 0.36466 (58) gca peak Right_choroid_plexus = 0.09865 (51) gca peak Fifth_Ventricle = 0.66382 (40) gca peak WM_hypointensities = 0.12408 (82) gca peak non_WM_hypointensities = 0.07897 (54) gca peak Optic_Chiasm = 0.38389 (74) Segmentation fault [swmed-xryrdix93:CorrectedBrainsGE/TBI/St43] teresa% --------- I can forward a recon-all.log of this subject. I've also had some major issues with intensity inhomogeneities where the pial, wm, and orig surfaces will not pick up the sulci in certain regions of the cortex (the wm -aux volume just looks like one big blob of grey). I've tried using -nuiterations 4, 150, etc., but have not had much success. Any suggestions would be greatly appreciated. Warm Regards, -t Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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error while loading shared libraries:libtiff.so.3
by Lúcia Garrido 30 Mar '08

30 Mar '08

Hello, I'm using Debian and downloaded freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz. Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all -i C04_SS.nii -autorecon1 -s C04_SS and it also finished without errors. But when I ran recon-all -autorecon2 -s C04_SS, there was an error at the end saying: mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory I've checked the shared libraries and I have libtiff.so.4. Could you let me know how to get libtiff.so.3 to work and if I should do something else? Thank you very much. Lucia

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[Fwd: Re: [Freesurfer] Error]
by jake＠nmr.mgh.harvard.edu 28 Mar '08

28 Mar '08

Hi, Thanks for the bugr command. Here is my information, Thank you! Please include the following additional information in your report: 1) subject name: CD_aftbotox_ctrl5 2) the entire command-line executed csh CD_aftbotox_ctrl5_ContrastAnalysis.csh 3) the error message generated (please see below, our preprocessing step is built into our csh file.) 4) optionally include the subject's /script/recon-all.log **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) PWD: /homes/14/jake/AnalysisPrograms --------------------------------------------------------------------- ---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error From: "Pratap Kunwar" <pkunwar(a)nmr.mgh.harvard.edu> Date: Fri, March 28, 2008 12:00 pm To: jake(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Jake, Are you doing preprocessing or stxgrinder, and are you running from > *running from the following directory > /autofs/homes/014/jake/AnalysisPrograms or /autofs/space/meso_018/users/ablood/cerv/ ? it will be nice if you provide more info. use "bugr" to get report and send to freesurfer. about bugreporting, https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&val… pratap > Hi, > > We are getting an error where our preprocessing step seems to be failing, > any help would be greatly appreciated, thank you! > > > > *using the following command (which sources > /usr/local/freesurfer/nmr-stable3-env) > striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > *error: > --- Parsing Config File: > /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg > ---- > -gammafit 2.25 1.25 -timewindow 25.0000 -prestim 0 -polyfit 1 -TER 2.5000 > -nskip 0 -fwhm 0 -rescale 1000 > ERROR: 022/fmcsm4 does not have a .meanval file, run inorm > ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): > selxavg failed > ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat > -------------------------------------------------------------- > stxgrinder-sess logfile is > /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log > -------------------------------------------------------------- > ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 > > > > > > > > **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > ***Here is the error from the logfile: > to3d WARNING: > Significant outliers detected in these sub-bricks: > 60 103 104 105 106 107 108 120 122 > You should inspect the dataset for possible corruption. > [Outliers are defined as in program 3dToutcount. ] > [Outliers early in an EPI time series may be due to ] > [the longitudinal magnetization equilibration effect.] > [Other causes are subject movement, scanner problems,] > [or anything that makes a time series look irregular.] > [ 3dToutcount -save outnam dataset | 1dplot -stdin ] > [can be used to make a dataset 'outnam' that marks ] > [outlier voxels; see 3dToutcount -help for details. ] > > ++ 3D dataset written to disk > -------------- Motion Correcting --------------------------- > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp > set VR = 3dvolreg > 3dvolreg -verbose -dfile > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct > rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] > 6776+orig > ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] > ++ Authored by: RW Cox > ++ Reading in base dataset ./targ-6776+orig.BRIK > ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same > dimensi > ons! > Input: nx=64 ny=64 nz=30 > Base: nx=64 ny=64 nz=16 > ** FATAL ERROR: perhaps you could make your datasets match? > set st = 1 > if ( 1 ) then > echo ERROR: 3dvolreg existed with status 1 > ERROR: 3dvolreg existed with status 1 > exit 1 > ERROR: mc-sess failed > > > > > Thanks, > > Jake > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Error
by jake＠nmr.mgh.harvard.edu 28 Mar '08

28 Mar '08

Hi, We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you! *running from the following directory /autofs/homes/014/jake/AnalysisPrograms *using the following command (which sources /usr/local/freesurfer/nmr-stable3-env) striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh *error: --- Parsing Config File: /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 25.0000 -prestim 0 -polyfit 1 -TER 2.5000 -nskip 0 -fwhm 0 -rescale 1000 ERROR: 022/fmcsm4 does not have a .meanval file, run inorm ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): selxavg failed ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat -------------------------------------------------------------- stxgrinder-sess logfile is /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log -------------------------------------------------------------- ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 **The logfile for preprocessing can be found in: /autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log ***Here is the error from the logfile: to3d WARNING: Significant outliers detected in these sub-bricks: 60 103 104 105 106 107 108 120 122 You should inspect the dataset for possible corruption. [Outliers are defined as in program 3dToutcount. ] [Outliers early in an EPI time series may be due to ] [the longitudinal magnetization equilibration effect.] [Other causes are subject movement, scanner problems,] [or anything that makes a time series look irregular.] [ 3dToutcount -save outnam dataset | 1dplot -stdin ] [can be used to make a dataset 'outnam' that marks ] [outlier voxels; see 3dToutcount -help for details. ] ++ 3D dataset written to disk -------------- Motion Correcting --------------------------- /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp set VR = 3dvolreg 3dvolreg -verbose -dfile /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] 6776+orig ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ++ Reading in base dataset ./targ-6776+orig.BRIK ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same dimensi ons! Input: nx=64 ny=64 nz=30 Base: nx=64 ny=64 nz=16 ** FATAL ERROR: perhaps you could make your datasets match? set st = 1 if ( 1 ) then echo ERROR: 3dvolreg existed with status 1 ERROR: 3dvolreg existed with status 1 exit 1 ERROR: mc-sess failed Thanks, Jake

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purpose of creating own "average subject"
by Michael Harms 28 Mar '08

28 Mar '08

Hello, There have been numerous posts recently related to the creation of a study specific "average subject". I have a question about the purpose/motivation of this for surface-stream analysis/visualization that I was hoping someone could clarify. Specifically, my understanding is that the annotation/labels for any derived study specific average subject are determined by the "buckner40" gcs file (for the case of the desikan atlas). And similarly, the average surface (e.g., white, pial) and curvature-format files (e.g., curv, sulc, thickness) are registered across subjects via sphere.reg, which is determined by ?h.curvature.filled.buckner40.tif? So, since the annotation and registration for any study specific "average subject" is going to be determined by the "buckner40" set of subjects regardless of the specific subjects in a particular study, what is the purpose, advantage, or necessity for creating a study specific average subject? Or stated differently, since the whole FS approach for registering surfaces (and by extension parcellating the cortex) is based on the assumption that the "buckner40" set of subjects is an appropriate registration and parcellation target for ALL studies, what is the point of creating a study specific average rather than using the default 'fsaverage' (which has the advantage of being created from the same set of 40 subjects that drive the registration itself)? Please help me understand what I'm missing here. thanks, Mike H. P.S. Am I correct in presuming that the same 40 subjects were used for the Desikan GCS atlas and for deriving the spherical registration (.tif) target? -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Label boundary
by SHRIKANTH KULASHEKHAR 28 Mar '08

28 Mar '08

Hi, Is there any freesurfer utility to isolate/plot the vertices that form the boundary of any label ? If no, how can one go about doing this ? Thank you. Shriks Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.php

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Parcellation Protocol?
by Raymond Hill 27 Mar '08

27 Mar '08

Hello, We are trying to compare FreeSurfer's parcellation with what we do here manually. To that end, we were wondering if we could access a detailed protocol that was used to manually create the ROIs that went into the FS Parcellation atlas? We have examined the Desikan et al (2006) paper with the brief descriptions but these are not particularly detailed. If this is not possible, is there any way we could find out the ways in which this atlas diverges from the standard CMA? Thank you! Ray Hill

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Talairach transformation
by Thomas Doering 27 Mar '08

27 Mar '08

Dear List, I got stucked when running the first recon step. There seems something wrong with the Tailarach Transformation step...But i don´t know how to fix it... I attached the recon-all file. Thanks for help, suggestions, etc. Cheers, Thomas

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Cluster on Demand
by Pedro Paulo Oliveira Jr 26 Mar '08

26 Mar '08

Dear Freesurfers I was testing a Cluster-on demand, pay-per-hour-used service US based and it seems pretty good. I ran 100 recon-all in 33 hours!!! The cost of one hour of CPU is USD 0.77 The quote I received is a package of 200.000 hours / month with an hour priced as USD 0.25 cents This figure represents 5500 Freesurfer recon-all per month. If many people in the list are interested in sharing the expenses I think it would be a quick way to process tons of brains. The info I received is that this cluster is based in Florida and have 300 cpus Hope this helps, PPJ

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Recon-all recent errors
by lbotelho＠nmr.mgh.harvard.edu 26 Mar '08

26 Mar '08

Hi, Since March, recon-all exits with errors on mris_extract_main_component. This happens when analyzing the same data with the same input commands used successfully prior to March. -------------------------------------------- >From the RECON-ALL.LOG: mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix ERROR: MRISread: file '../surf/lh.orig.nofix' has more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory Linux node0241 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Mar 25 12:43:45 EDT 2008 -------------------------------------------- >From RECON-ALL.ERROR: $Id: recon-all,v 1.179 2008/03/19 20:11:52 greve Exp $ /usr/local/freesurfer/dev/bin/recon-all PWD /autofs/space/heisenberg_005/users/lbotelho/subjects/DBS_C12_15T_r2repeat/scripts CMD mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix -------------------------------------------- I wonder if this may be related with the updated Freesurfer development version and about the best way to fix it. Thank you, Luis

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