External Email - Use Caution At all other smoothing and threshold combinations, the simulations indicate that there are no significant clusters on the lateral surface of the left hemisphere, but there is a large cluster on the medial surface (lingual gyrus). For 10mm+th.13, however, the simulation indicates there is a large cluster on the lateral surface (supramarginal gyrus), but no significant cluster on the medial surface. All cluster.summary files have been attached to this email (smoothing at 10mm, thresholds 1.3, 2.0, 2.3, and 3.0) in case they are helpful.
Having a significant cluster at a lower threshold (i.e., 1.3), but not at a more stringent threshold makes sense. But I’m not sure why the lingual gyrus cluster isn’t present at 1.3 when it is present at more stringent thresholds. Any guidance or suggestions are appreciated! Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology julia...@uab.edu<mailto:julia...@uab.edu> On Mar 13, 2020, at 5:49 PM, Douglas N. Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote: Can you say more about how the 10mm, th 1.3 is different than the others? On 3/11/2020 2:48 PM, Purcell, Juliann wrote: External Email - Use Caution Hi FreeSurfer Experts, I am running permutation simulations with several smoothing levels and cluster forming thresholds to evaluate the best parameters for our data, since there does not seem to be a consensus in the literature. However, I’m getting an unexpected result at only one smoothing/threshold level. I have run permutations (mri_glmfit-sim) at 0mm, 5mm, 10mm using the following thresholds: 1.3, 2.0, 2.3, and 3.0. Results of permutation at 10mm + threshold 1.3 were not as expected and did not line up with results at the other smoothing and threshold levels. I’ve re-checked that the command is correctly referencing the data and I’ve compared the th1.3 log file with the log files at the other thresholds. I could not find any differences that would cause the output of the permutation simulations to be so different between th1.3 and th2.0. There are no errors or failures in the permutation log files. I’ve searched the message board and didn’t see any posts that related to this issue. Although it’s possible that these are true results, I want to make sure there isn’t a mistake on my end. Any help would be greatly appreciated! Below is information about my FreeSurfer version, platform, and the log files from the permutation simulations: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Linux 3) uname -a: Linux c0135 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 EST 2019 x86_64 x86_64 x86_64 GNU/Linux 4) Perm sim log files: See attached logs for 10mm smoothing at threshold 1.3 and threshold 2.0 Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology julia...@uab.edu<mailto:julia...@uab.edu> _______________________________________________ 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
perm.th13.abs.sig.cluster.summary
Description: perm.th13.abs.sig.cluster.summary
perm.th20.abs.sig.cluster.summary
Description: perm.th20.abs.sig.cluster.summary
perm.th23.abs.sig.cluster.summary
Description: perm.th23.abs.sig.cluster.summary
perm.th30.abs.sig.cluster.summary
Description: perm.th30.abs.sig.cluster.summary
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