The mri_glmfit command below is for the left hemisphere. so I don't understand when you later say that you run it again on the left hemi but get an error. Can you post just the command that you ran that gave the error as well as the terminal output for that command?
On 4/27/15 4:17 PM, Alshikho, Mohamad J. wrote: > I ran only one command line : > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C > Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C > Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls > --nii.gz > > This command ran smoothly on the right hemisphere so I ran the second command > : > > mri_glmfit-sim --glmdir glm-fsgd-2G0C.wls --cache 3 pos --cwpvalthresh 0.166 > > > But when I run the first command line on the left hemisphere using the same > FSGD file and the same contrast I receive the following message : > > INFO: gd2mtx_method is dods > Saving design matrix to glm-fsgd-2G0C.wls/Xg.dat > Computing normalized matrix > Normalized matrix condition is 1 > Matrix condition is 2.5 > Found 149955 points in label. > Pruning voxels by thr: 1.175494e-38 > Found 148773 voxels in mask > Saving mask to glm-fsgd-2G0C.wls/mask.nii.gz > Reshaping mriglm->mask... > search space = 74067.765554 > DOF = 12 > Starting fit and test > Fit completed in 0.115333 minutes > Computing spatial AR1 on surface > WARNING: ar1 = 0 <= 0. Setting fwhm to 0. > Residual: ar1mn=0.000000, ar1std=0.000000, gstd=0.000000, fwhm=0.000000 > Writing results > Contrast1group.diff > maxvox sig=1e+10 F=0 at index 204 0 0 seed=1430655459 > MatrixMultiply: m2 is null! > > > I can't figure out what is the meaning what is the message > > > > > > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, April 27, 2015 4:10 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_ functional connectivity analysis > > can you send the two command lines you ran? > > On 04/27/2015 02:53 PM, Alshikho, Mohamad J. wrote: >> Hi Doug, >> I am working on a GLM for functional connectivity analysis. I made simple >> FSGD file for two groups + NO covariates then I ran the following command >> line on the right hemisphere and the left hemisphere. >> >> >> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C >> Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C >> Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir >> glm-fsgd-2G0C.wls --nii.gz >> >> >> On the right hemisphere the output is fine for all the contrasts. >> >> >> On the left hemisphere and after writing the results for contrast 1 I am >> receiving the following message: >> >> MatrixMultiply: m2 is null! >> >> >> Kindly what is the meaning of this message? >> >> >> Thanks, >> Mohamad >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
