Hi,
I'm getting a segmentation fault when trying to do a group contrast using glmfit. I think it's likely to be the parameters I'm using, because this is this is the first time I've tried to do this. This seems correct, but I don't know for sure. I've included the evironment/command/output info below and below that the contents of my fsgd file.
Thanks, Rob
[levy@vantz ~]$ cd $SUBJECTS_DIR/ [levy@vantz SUBJECTS_DIR]$ use_dev -------- freesurfer-Linux-centos4_x86_64-dev-20070706 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) mri_glmfit \ ? --really-use-average7 \ ? --y lh.ASvfix_8s_BwGroupError5.fsfast.mgh \ ? --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ ? --glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir \ ? --pca \ ? --surf average7 lh \ ? --C fsgd_and_contrast_files/BwGroupError5.mat gdfReadHeader: reading fsgd_and_contrast_files/BwGroupError5.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 Normals 2 ASD INFO: gd2mtx_method is dods
INFO: you have selected subject average7 (and REALLY want to use it) instead of fsaverage. So I'm going to turn off fixing of vertex area to maintain compatibility with the pre-stable3 release.
Reading source surface /space/ventzl/1/users/SUBJECTS_DIR/average7/surf/lh.whiteNumber of vertices 163842 Number of faces 327680 Total area 63393.164062 AvgVtxArea 0.386916 AvgVtxDist 0.710285 StdVtxDist 0.246011
$Id: mri_glmfit.c,v 1.134 2007/06/24 21:05:52 greve Exp $ cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR cmdline mri_glmfit --really-use-average7 --y lh.ASvfix_8s_BwGroupError5.fsfast.mgh --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd --glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir --pca --surf average7 lh --C fsgd_and_contrast_files/BwGroupError5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 0 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/space/ventzl_001/users/SUBJECTS_DIR/lh.ASvfix_8s_BwGroupError5.fsfast.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupError5.fsgd glmdir lh.ASvfix_8s_BwGroupError5.fsfast.glmdir DoFFx 0 Creating output directory lh.ASvfix_8s_BwGroupError5.fsfast.glmdir Loading y from /autofs/space/ventzl_001/users/SUBJECTS_DIR/lh.ASvfix_8s_BwGroupError5.fsfast.mgh Matrix condition is 1 Pruning voxels by frame. Found 153159 voxels in mask Saving mask to lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/mask.mgh search space = 59259.7 DOF = 22 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.03595 minutes Computing spatial AR1 on surface Residual: ar1mn=0.948094, ar1std=0.034478, gstd=1.538271, fwhm=3.622352 Writing results BwGroupError5 maxvox sig=-4.67846 F=28.9727 at index 14025 0 0 seed=1184295814 Computing PCA (24) Segmentation fault [vantz:SUBJECTS_DIR] (nmr-dev-env)
Contents of fsgd file:
[levy@vantz ~]$ cat $SUBJECTS_DIR/fsgd_and_contrast_files/BwGroupError5.fsgd GroupDescriptorFile 1 Title HCvASD Class Normals Class ASD
Input mano001 Normals Input mano002 Normals Input mano004 Normals Input mano005 Normals Input mano007 Normals Input mano008 Normals Input mano009 Normals Input mano010 Normals Input mano011 Normals Input mano012 Normals Input mano013 Normals Input mano014 Normals Input mano016 Normals Input mano025 Normals Input manoA02 ASD Input manoA03 ASD Input manoA04 ASD Input manoA05 ASD Input manoA07 ASD Input manoA08 ASD Input manoA09 ASD Input manoA10 ASD Input manoA11 ASD Input manoA13 ASD