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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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
Re: [Freesurfer] GLM_ functional connectivity analysis
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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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 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
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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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.
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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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
Re: [Freesurfer] GLM_ functional connectivity analysis
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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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
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 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.
Re: [Freesurfer] GLM_ functional connectivity analysis
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=0.00, ar1std=0.00, gstd=0.00, fwhm=0.00 Writing results Contrast1group.diff maxvox sig=1e+10 F=0 at index 204 0 0seed=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 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.
[Freesurfer] GLM_ functional connectivity analysis
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 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.
