Hi everyone,
I get this error when running group analysis of cortical thickness by command-line:
xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir gdfReadHeader: reading group_differ.fsgd INFO: gd2mtx_method is dods Reading source surface /media/E/FREESURFER/VisualData/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 /media/E/FREESURFER/VisualData cmdline mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir sysname Linux hostname xinfa--PC machine x86_64 user xin-fa FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh logyflag 0 usedti 0 FSGD group_differ.fsgd labelmask /media/E/FREESURFER/VisualData/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.group_differ.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.group_differ.glmdir Loading y from /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.group_differ.glmdir/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.04762 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to lh.group_differ.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 ERROR: dimension mismatch between X and contrast con.mtx X has 2 cols, C has 1 cols
The data is altogether 43 subjects,including 22 subjects in expert group.I just want to explore the difference between both groups. Attached is the FSGD file ,which is two groups ,zero covariates . The contrast matrix is 1 -1 .
Subsequently I try it only with a few subjects ,and it succeeds. Can you help me ?
Best wishes.
Xin-Fa .
It says that C has only one column. Make sure that you created the C matrix as a simple text file. Don't create it on Windows or with a word processor. An easy way to create it is echo 1 -1 > con.mtx
doug
On 11/26/14 9:44 PM, Xinfa Shi wrote:
Hi everyone,
I get this error when running group analysis of cortical thickness by command-line:
xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir gdfReadHeader: reading group_differ.fsgd INFO: gd2mtx_method is dods Reading source surface /media/E/FREESURFER/VisualData/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 /media/E/FREESURFER/VisualData cmdline mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir sysname Linux hostname xinfa--PC machine x86_64 user xin-fa FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh logyflag 0 usedti 0 FSGD group_differ.fsgd labelmask /media/E/FREESURFER/VisualData/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.group_differ.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.group_differ.glmdir Loading y from /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.group_differ.glmdir/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.04762 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to lh.group_differ.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 ERROR: dimension mismatch between X and contrast con.mtx X has 2 cols, C has 1 cols
The data is altogether 43 subjects,including 22 subjects in expert group.I just want to explore the difference between both groups. Attached is the FSGD file ,which is two groups ,zero covariates . The contrast matrix is 1 -1 .
Subsequently I try it only with a few subjects ,and it succeeds. Can you help me ?
Best wishes.
Xin-Fa .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Xinfa Shi