Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right?
Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong?
There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial:
[lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt--glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731
$Id: mri_glmfit.c,v 1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done
------------ This is my FSGDF:
$ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ
Lars,
After loading the statistical parametric map overlay file that was created, did you select a vertex on the surface displayed in tksurfer? That should bring-up the data for that point in the plot window. I wasn't sure from your email if this was attempted. I'll look into answering your specific questions about the output.
Nick
Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right?
Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong?
There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial:
[lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt--glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731
$Id: mri_glmfit.c,v 1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done
This is my FSGDF:
$ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ
-- yours, LMR _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Not sure why you could not load the fsgd, but the other stuff looks correct. Smaller condition numbers are better, with the best being 1 and something like 1000 being pretty bad. DOF=8 is probably correct if you had two groups (which would preclude a one-sample group mean). It should not take more than a minute to run unless you are smoothing or simulating.
doug
Lars M. Rimol wrote:
Hi, I did a group analysis on 10 subjects (as a test run) following the steps of the updated tutorial. I get no error messages, however, when I load the y.fsgd, there are no data points. These 10 subjects were chosen randomly, solely for the purpose of running through the group analysis procedure, so I don't necessarily expect significant findings but at least there shold be some datapoints, right?
Make_average_subject, mris_preproc and mri_surf2surf went fine without error messages but the mri_glmfit script took less than 1 minute to run, which I think seems a little suspicious. What should "Matrix condition" be? Here, it was 1. And DOF? (It was 8). Is "OneSampleGroupMean 0" a sign that something has gone wrong?
There was a warning message during mri_glmfit, but the fsgdf is in accordance with the tutorial:
[lmr@ip45 ovelse]$ mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf average rh --C contrast.mat gdfReadHeader: reading IQ.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /home/subjects/average/surf/rh.white reading group avg surface area 948 cm^2 from file Reading in average area /home/subjects/average/surf/rh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 78857.140625 AvgVtxArea 0.481300 AvgVtxDist 0.814244 StdVtxDist 0.276731
$Id: mri_glmfit.c,v MailScanner has detected a possible fraud attempt from "1.78.2.5" claiming to be MailScanner warning: numerical links are often malicious: 1.78.2.5 http://1.78.2.5 2006/03/10 23:27:29 greve Exp $ cwd /home/subjects/ cmdline mri_glmfit --y rh.IQ.txt.thickness.10.mgh --fsgd IQ.txt --glmdir rh.IQ.txt.glmdir --pca --surf averageja rh --C contrast.mat sysname Linux hostname ip45.ucsd.edu http://ip45.ucsd.edu machine x86_64 user lmr FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /home/subjects/rh.IQ.txt.thickness.10.mgh FSGD IQ.txt glmdir rh.IQ.txt.glmdir Creating output directory rh.IQ.txt.glmdir Loading y from /home/subjects/rh.IQ.txt.thickness.10.mgh Matrix condition is 1 search space = 94836.7 DOF = 8 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 0.0191 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995564, ar1std=0.004225, gstd=6.106113, fwhm=14.378798 Writing results contrast maxvox sig=-3.35122 F=32.6872 at index 22070 0 4 seed=1149137562 Computing PCA (10) mri_glmfit done
This is my FSGDF:
$ cat IQ_fsgdf.txt GroupDescriptorFile 1 Title Gruppesammenligning Class lowIQ Class highIQ Variables Input TOP_161 lowIQ Input TOP_162 lowIQ Input TOP_163 lowIQ Input TOP_164 lowIQ Input TOP_165 lowIQ Input TOP_166 highIQ Input TOP_167 highIQ Input TOP_175 highIQ Input TOP_188 highIQ Input TOP_189 highIQ
-- yours, LMR
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Lars M. Rimol -
Nick Schmansky