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Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that.
I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2.
This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
Any advice would be appreciated! Caspar
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Hi! Any advice on this issue? The error message is:
Starting contrasts UrInv J=1 ------------- Out of memory. Type "help memory" for your options.
Error in fast_glm_pcc (line 39) yhatd = Rd*(X*beta);
Error in fast_fratiow (line 136) if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin); end
Error in fast_selxavg3b (line 1148) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));
ERROR: fast_selxavg3() failed\n
Thank you, Caspar
Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik < cschwiedrz@rockefeller.edu>:
Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that.
I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2.
This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
Any advice would be appreciated! Caspar
Sorry, I thought I sent an email responding to this. Try running it with -run-wise. This will analyze each run separately. I can't remember whether it generates a final combined average (been a long time since I used this option), but run it and see what it does.
On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi! Any advice on this issue? The error message is:
Starting contrasts UrInv J=1 ------------- Out of memory. Type "help memory" for your options.
Error in fast_glm_pcc (line 39) yhatd = Rd*(X*beta);
Error in fast_fratiow (line 136) if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin); end
Error in fast_selxavg3b (line 1148) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));
ERROR: fast_selxavg3() failed\n
Thank you, Caspar
Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu:
Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2. This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory. Any advice would be appreciated! Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug, thanks for the advice! I can compute the GLM and contrasts per run. But selxavg3 does not compute contrasts across the runs with per-run. Could you give me some advice on how to concatenate the per run contrasts - can I just append them and add the df degrees of freedom? Thanks, Caspar
Am Fr., 24. Juni 2022 um 16:36 Uhr schrieb Douglas N. Greve < dgreve@mgh.harvard.edu>:
*Caution: External email* Sorry, I thought I sent an email responding to this. Try running it with -run-wise. This will analyze each run separately. I can't remember whether it generates a final combined average (been a long time since I used this option), but run it and see what it does.
On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote:
External Email - Use CautionHi! Any advice on this issue? The error message is:
Starting contrasts UrInv J=1 ------------- Out of memory. Type "help memory" for your options.
Error in fast_glm_pcc (line 39) yhatd = Rd*(X*beta);
Error in fast_fratiow (line 136) if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin); end
Error in fast_selxavg3b (line 1148) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));
ERROR: fast_selxavg3() failed\n
Thank you, Caspar
Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik < cschwiedrz@rockefeller.edu>:
Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that.
I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2.
This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
Any advice would be appreciated! Caspar
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You can try running mri_glmfit to run a fixed effects analysis fist, concatenate all the ces.nii.gz files (mri_concat */ces.nii.gz --o all.ces.nii.gz) second, do the same for the cesvar.nii.gz files third, compute total dof (see the dof.dat files in each run folder) 4th, mri_glmfit --y all.ces.nii.gz --yffxvar all.cesvar.nii.gz --ffxdof DOFtotal --osgm --glmdir glmdiroutput If you want to do a higher level analysis, then you will have to do it by hand (ie, not using isxconcat-sess)
On 6/25/2022 4:57 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi Doug, thanks for the advice! I can compute the GLM and contrasts per run. But selxavg3 does not compute contrasts across the runs with per-run. Could you give me some advice on how to concatenate the per run contrasts - can I just append them and add the df degrees of freedom? Thanks, Caspar
Am Fr., 24. Juni 2022 um 16:36 Uhr schrieb Douglas N. Greve dgreve@mgh.harvard.edu:
*Caution: External email* Sorry, I thought I sent an email responding to this. Try running it with -run-wise. This will analyze each run separately. I can't remember whether it generates a final combined average (been a long time since I used this option), but run it and see what it does. On 6/23/2022 2:00 PM, Caspar M. Schwiedrzik wrote:External Email - Use Caution Hi! Any advice on this issue? The error message is: Starting contrasts UrInv J=1 ------------- Out of memory. Type "help memory" for your options. Error in fast_glm_pcc (line 39) yhatd = Rd*(X*beta); Error in fast_fratiow (line 136) if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin); end Error in fast_selxavg3b (line 1148) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:)); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you, Caspar Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu>: Hi! I am running large single subject GLMs with selxavg3-sess and I run into a Matlab "out of memory" error. I was wondering whether you had any advice on how to get around that. I have 40-50 runs per subject, and the analyses are whole brain. The GLM per subject runs through fine, but the error occurs once selxavg3-sess starts computing contrasts. The problem occurs with v5.3 and v7.2. This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory. Any advice would be appreciated! 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