PALM handles GIFTI and CIFTI data. Peace,
Matt. On 8/29/16, 6:21 PM, "Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >Does PALM do surface-based? Also, there is no way to appropriately >handle this. For permutation, non-orthogonal designs are wrong. There >are ways to try to compensate for it, which is what PALM is doing. Sorry >to be nit-picky! > > >On 08/29/2016 06:12 PM, Harms, Michael wrote: >> Hi Maaike, >> Why not just use PALM? Then you don¹t have to worry about this (since >> PALM appropriately handles the situation of correlated covariates). >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 >> St. Louis, MO 63110Email: mha...@wustl.edu >> >> >> >> >> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>of >> Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> gr...@nmr.mgh.harvard.edu> wrote: >> >> It is hard to say. Since the subjects are not exchangeable, the >> permutation is technically not appropriate. Check the winkler paper, I >> think he talks about what happens if you just don't do anything. >> >> >> On 08/29/2016 11:07 AM, maaike rive wrote: >>> Hi all, >>> >>> >>> Is using forced permutation for non-orthogonal design matrices wrong >>> or is it allowed to do this instead of using tools like palm (what >>> happens eg with the covariates when using forced permutation)? I >>> used forced permutation and it seemed to work, results were (partly) >>> comparable to what I found with monte carlo simulations. >>> >>> >>> Thanks, Maaike >>> >>> >>>------------------------------------------------------------------------ >>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >>> <mha...@wustl.edu> >>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 >>> *Aan:* Freesurfer support list >>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing >>> running after 3 days! >>> >>> Hi, >>> You might want to check out FSL¹s PALM tool, which has a bit more >>> sophisticated permutation framework, and allows for permutation in the >>> context of non-orthogonal covariates. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> ----------------------------------------------------------- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> From: <freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ajay >>> Kurani <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> >>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Date: Thursday, August 25, 2016 at 4:13 PM >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running >>> after 3 days! >>> >>> 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? >>> >>> 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? >>> >>> 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.ht >>>ml >>> >>> >>><http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.h >>>tm >>> l> >>> ) >>> >>> 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-t >>>hi >>> ckness.mtx >>> --C >>> >>> >>>./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Femal >>>e- >>> Intercept-thickness.mtx >>> --C >>> >>> >>>./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Int >>>er >>> cept-thickness.mtx >>> --C >>> >>> >>>./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group- >>>In >>> tercept-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.m >>>gh >>> --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 >>> >>> >>> >>>------------------------------------------------------------------------ >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on >>> the contents of this information is strictly prohibited. If you have >>> received this email in error, please immediately notify the sender via >>> telephone or return 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 >> >> >> 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. >> >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >>Healthcare Information or other information of a sensitive nature. If >>you are not the intended recipient, be advised that any unauthorized >>use, disclosure, copying or the taking of any action in reliance on the >>contents of this information is strictly prohibited. If you have >>received this email in error, please immediately notify the sender via >>telephone or return 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
