Can you tar up all the input files and send them to me through our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2 doug On 04/28/2015 11:36 AM, Alshikho, Mohamad J. wrote: > 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 rh --glmdir glm-fsgd-2G0C.wls > --nii.gz > > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve > Sent: Tuesday, April 28, 2015 10:47 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_ functional connectivity analysis > > What was the exact command for the right hemi? > > On 4/28/15 10:45 AM, Alshikho, Mohamad J. wrote: >> Hi Doug, >> Thank you for your support. >> >> I ran this command on 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 I got the error >> message : MatrixMultiply: m2 is null! >> >> and I ran the same command on the right hemisphere by replacing (--surface >> fsaverage lh) by (--surface fsaverage rh) and it was fine. >> >> >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> Greve >> Sent: Tuesday, April 28, 2015 10:39 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] GLM_ functional connectivity analysis >> >> >> 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 >> >> _______________________________________________ >> 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 > > -- 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 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.
