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
[EMAIL PROTECTED] ~]$ cd $SUBJECTS_DIR/
[EMAIL PROTECTED] SUBJECTS_DIR]$ 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:
[EMAIL PROTECTED] ~]$ 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
--
Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2656
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
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