Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering each subject’s contrast as an overlay, and would now like to compute the group-level results.
I first ran isxconcat-sess, and saw no errors indicated in the program output.
mri_glmfit was then called as followed, and produced the following output (same result for the rh):
$ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz Reading source surface /home/chris/LDT/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz sysname Linux hostname brocasarea machine x86_64 user chris FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz logyflag 0 usedti 0 labelmask /home/chris/LDT/fsaverage/label/lh.cortex.label maskinv 0 glmdir glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory glm.wls Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz Saving design matrix to glm.wls/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 537168 Pruning voxels by thr: 0.000000 Segmentation fault (core dumped)
This seems to have its root in a mismatch between the vertices in the fsaverage lh.cortex label and those in the contrast data. However, I carried out subject-level analyses in the fsaverage surface space specifically to facilitate a group-level analysis in fsaverage surface space, so I can’t see where I went wrong. The only other post I could find that was similar was related to an attempt to carry out a group analysis in native surface space, which is not the case here.
Thanks for your time
not sure what is going wrong. Does it work if you do not include the --wls cesvar.nii.gz ?
On 6/28/17 12:29 PM, Mcnorgan, Christopher wrote:
Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering each subject’s contrast as an overlay, and would now like to compute the group-level results.
I first ran isxconcat-sess, and saw no errors indicated in the program output.
mri_glmfit was then called as followed, and produced the following output (same result for the rh):
$ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz Reading source surface /home/chris/LDT/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz sysname Linux hostname brocasarea machine x86_64 user chris FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz logyflag 0 usedti 0 labelmask /home/chris/LDT/fsaverage/label/lh.cortex.label maskinv 0 glmdir glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory glm.wls Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz Saving design matrix to glm.wls/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 537168 Pruning voxels by thr: 0.000000 Segmentation fault (core dumped)This seems to have its root in a mismatch between the vertices in the fsaverage lh.cortex label and those in the contrast data. However, I carried out subject-level analyses in the fsaverage surface space specifically to facilitate a group-level analysis in fsaverage surface space, so I can’t see where I went wrong. The only other post I could find that was similar was related to an attempt to carry out a group analysis in native surface space, which is not the case here.
Thanks for your time
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Douglas Greve -
Mcnorgan, Christopher