Re: [Freesurfer] Permutation output
The log file ends abruptly. Try the following mri_glmfit-sim --debug --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg | tee doug.log and send me doug.log doug On 08/11/2015 07:02 AM, pablo najt wrote: Thanks. Sorry but I am not being able to figure it out yet. Basically I am not getting the expected outcome. So I thought to give you an idea of how I am running permutations. mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg And I am attaching a snapshot of the output files and the log of mdi_glmfit-sim. At this stage I am wondering whether in order to run permutation it is required use as input the output from fsgd rather than qdec, because my input is from qdec. Would this make any difference? Thanks. Pablo Date: Mon, 10 Aug 2015 11:13:13 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permutation output It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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
Re: [Freesurfer] Permutation output
It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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] Permutation output
Thank you Doug.I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output.Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ 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 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.
