Something strange is going on in your data. You are using fsaverage, but the size of the data in PDvsMCI_lh_thickness_10mm/y.mgh does not match (it has 148278 vertices, not 163842 of fsaverage). This is causing the processes to die, but the backgrounding software does not know that the process died and so just keeps polling.
What I don't understand is why the original call to mri_glmfit did not die too. When I run it as such, it does die. It may be that the data in that folder did not get deleted by QDEC, and there is a strange mix of data in there. Can you delete that folder and try it again? Also, don't run it in background mode until you know that it is working. On 08/25/2016 01:18 PM, Ajay Kurani 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 > ) > > 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.
