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" <[EMAIL PROTECTED]> Date: Fri, March 28, 2008 12:00 pm To: [EMAIL PROTECTED] -------------------------------------------------------------------------- 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&value=bugr 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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
