On 08/25/2016 05:13 PM, Ajay Kurani wrote: > Hi Doug, > Thanks for the help! I think I figured out the issue based on your > response. > 1) I created a template to use for this group and named it fsaverage > (including creating monte carlo simulations) for simplicity of > integrating with freesurfer as I am newer to it. This is why the > sizes didn't match up as you expected > but the mri_glmfit still ran. > > 2) I deleted the folder and restarted without background processes. > The error became apparent. Of my covariates (2 fix factors and 3 > quantitative), not all were orthogonal. In looking at the error more, > it seems that i need to add the > --perm-force if I wanted the simulation to run, however the background > processes were not aware of this error and kept polling as you mentioned. > > This brings me to a new but related issue. From what I have read in > other freesurfer posts, it is statistically incorrect to use > --perm-force for non-orthogonal covariates (or continuous > covariates). I am unsure how to proceed. > a) If I ran permutation testing (to overcome the issue of incorrect > smoothness estimations from the gaussian distribution assumption), > then I run into the issue of non-orthogonal covariates. Is there a > way to orthogonalize the data in > freesurfer, or a solution to this issue? There are ways to do this, but I don't have them implemented yet. See here http://www.ncbi.nlm.nih.gov/pubmed/24530839 > > b) If orthogonalizing is difficult to implement, another option is > running Qdec with the montecarlo simulation at a more conservative p > value (p< 0.001). From your previous posts, the testing at this p > value for 10mm seems to meet the 5% FPR. One question is if the > non-orthogonal data affects this analysis as well for this model? No,non-orthogonalality has no effect on the monte carlo analyis > > Thanks, > Ajay > > On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani > <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> wrote: > > Hi Freesurfer Experts, > I am trying to use freesurfer's mri_glmfit-sim tool to run > permutation testing on cortical thickness data (as recommended by > Doug in my previous post: > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html > > <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html> > ) > > Most of the tutorials I found were not related to permutation > testing so the subsequent steps may be incorrect. Please let me > know where I go wrong... > > 1) I first ran QDec to generate a folder for the analysis which > would create the subsequent fsgd and y files needed my > mri_glmfit-sim. I am running both left and right hemisphere > cortical thickness analysis with 10mm smoothing. The following is > for just the left hemisphere. Note I am doing a 3 group > comparison, but for this 2 group ttest I manually centered the > data based on the 3 group mean for age and education. > > 2) I ran the following command: > /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm > 10000 2 perm.abs.2 --sim-sign abs --bg 16 > > Prior to running the command above, from the y.fsdg file I deleted > the fwhm estimate of 13mm since this was not correctly estimated > (ACF with long tails). I assumed that by removing this estimate, > it would force the permutation test to calculate based on the data > but when looking at the log output I see the following which says > fwhm 0: > > cmdline mri_glmfit.bin --C > > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx > --C > > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx > --C > > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx > --C > > ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx > --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 > --y > /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh > --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm > 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage > lh white --sim-done > ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 > > 3)I started this a few days ago on a 16 core machine and it is > still running in the terminal. I have 150 subjects in the > analysis and specified 10000 iterations. In the terminal I > assumed when I reach Poll 10000 it would be complete but currently > I am at : Poll 13341 job 1 Thu Aug 25 12:03:51 CDT 2016 > > Questions: > a) I am curious, is this going to run 10,000 simulations X 150 > patients or does the Poll number not have anything to do with the > number of iterations it is on? > > > b) Did I run this procedure correctly? Was I incorrect in > deleting the fwhm estimate from y.fsgd file generated by Qdec even > though we know the estimate is incorrect since smoothness assumed > a gaussian distribution as opposed to gaussian with heavy tails > > c) I noticed in the logfile the following warning: > INFO: gd2mtx_method is dods > Computing normalized matrix > Normalized matrix condition is 5.65727 > Matrix condition is 935.597 > Found 136777 voxels in mask > Reshaping mriglm->mask... > search space = 89675.729228 > ERROR: design matrix is not orthogonal, cannot be used with > permutation. > If this something you really want to do, run with --perm-force > Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 > > I am not sure if this means my simulation is incorrect? > > Thanks, > Ajay > > > > > _______________________________________________ > 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.
