I did not doug On 04/29/2015 01:19 PM, Alshikho, Mohamad J. wrote: > Hi Doug, > I sent you the files. I hope you got them > ________________________________________ > 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: Tuesday, April 28, 2015 11:43 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM_ functional connectivity analysis > > 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 > > _______________________________________________ > 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.
