Hi doug it's requesting the --sim option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments what args do I give the --sim! Jon ----- Original Message ----- From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> To: "Jon Wieser" <wie...@uwm.edu> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates sorry, it is --cwp On 12/13/2013 12:12 PM, Jon Wieser wrote: > HI Doug > MRI_glmfit-sim didn't recognize the --cwd option > > > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 > ERROR: Flag --cwd unrecognized. > --glmdir MTA_ADHD_MJ --cwd .99 > > > > > > > ----- Original Message ----- > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Friday, December 13, 2013 10:54:19 AM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > I'm sure that those clusters are not very significant. Try running > mri_glmfit-sim with --cwd .99 to capture all clusters > doug > > > On 12/12/2013 03:27 PM, Jon Wieser wrote: >> HI Doug, >> here's a screen shot, showing the clusters and a scatter plot for one of the >> 45 clusters. >> for this dataset, ussualy there is 0 or 1 clusters after monte carlo >> simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l >> have to look into that. >> >> I would like to have a file which contains the data represented in the >> scatter plot, for all of the 45 clusters, vlaues of thickness for each >> subject. is that possible? >> I tried runnin mri_surfcluster, but it only gave me the average data for >> that clusters, not the individual data. >> >> thanks! >> >> Jon >> >> ----- Original Message ----- >> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wie...@uwm.edu> >> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Thursday, December 12, 2013 1:15:58 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> I'm not sure what is going on. Can you send a screen shot of the qdec >> window when you see 40 clusters? It might be that it is showing clusters >> regardless of the cluster significance. Do the 3 or 4 clusters created >> when you run mri_glmfit-sim match clusters in qdec? >> >> On 12/10/2013 05:32 PM, Jon Wieser wrote: >>> Hi Doug >>> I'm looking at the effect of MJ usage, the effect of whetherthe subject >>> has AHDH, and the interaction between MJ usage and ADHD >>> our threshold is 1.3 >>> >>> i have attahced our qdec.table.dat file >>> we are also looking at age and gender as covariates >>> Jon >>> >>> Jon >>> ----- Original Message ----- >>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wie...@uwm.edu>, Freesurfer@nmr.mgh.harvard.edu >>> Sent: Tuesday, December 10, 2013 4:20:30 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> which contrast are you looking at in QDEC? Also, what is the voxel-wise >>> threshold in QDEC? The value I gave in the command below is 1.3 but I >>> got that from one of your CSD files. >>> >>> >>> On 12/10/2013 05:10 PM, Jon Wieser wrote: >>>> HI doug, >>>> no, the summary files in the contrasts have the same # of cluster >>>> as the columns in their OCN.dat \ >>>> the 40 cluster are seen in qdec when I run the "find cluster" and Goto >>>> max" button. most of these clusters go away in qdec when I run the >>>> montecarlo simulation >>>> >>>> Jon >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wie...@uwm.edu> >>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>> Sent: Tuesday, December 10, 2013 4:03:06 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> So one of the contrasts has 40 clusters in the summary file but the >>>> y.ocn.dat file only has a few columns? >>>> >>>> >>>> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>>>> yes, that is what we want, but the files contain only 1-3 columns >>>>> >>>>> Jon >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wie...@uwm.edu> >>>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>>> Sent: Tuesday, December 10, 2013 3:44:50 PM >>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>> >>>>> >>>>> There should be a column for each cluster in contrast. Is that what you >>>>> want? >>>>> >>>>> >>>>> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>>>>> thanks, >>>>>> I ran >>>>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>>>>> >>>>>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>>>>> >>>>>> >>>>>> it has produced: >>>>>> >>>>>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>>>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>>>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>>> >>>>>> >>>>>> >>>>>> these files have 120 rows. each row has a thickness value s >>>>>> example >>>>>> 2.71869 >>>>>> 2.52448 >>>>>> 2.50450 >>>>>> 2.53677 >>>>>> 2.58363 >>>>>> 2.50404 >>>>>> 2.42116 >>>>>> 2.61757 >>>>>> 2.51820 >>>>>> 2.59009 >>>>>> 2.42524 >>>>>> 2.72043 >>>>>> 2.59479 >>>>>> 2.38014 >>>>>> 2.41052 >>>>>> 2.58483 >>>>>> 2.49214 >>>>>> 2.45870 >>>>>> 2.51685 >>>>>> 2.62981 >>>>>> 2.59232 >>>>>> >>>>>> it appears that there is the thickness for each subject in the files >>>>>> >>>>>> I would like to have the thickness value, for each cluster, for every >>>>>> subject >>>>>> >>>>>> we have 120 subjects, with about 40 clusters >>>>>> Jon >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wie...@uwm.edu> >>>>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>>>> Sent: Tuesday, December 10, 2013 2:30:31 PM >>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>> >>>>>> >>>>>> OK, sorry, I thought qdec was running a script called mri_glmfit-sim but >>>>>> it appears to be running the correction internally. That means that you >>>>>> will have to run mri_glmfit-sim yourself, something like >>>>>> >>>>>> mri_glmfit-sim --glmdir glmdir --cache 1.3 abs >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 12/10/2013 02:53 PM, Jon Wieser wrote: >>>>>>> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log >>>>>>> in the qdec output directory >>>>>>> Jon >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wie...@uwm.edu>, Freesurfer@nmr.mgh.harvard.edu >>>>>>> Sent: Tuesday, December 10, 2013 1:42:37 PM >>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>> >>>>>>> >>>>>>> Is there a cache.mri_glmfit-sim.log in the output folder? Can you send >>>>>>> it to me? Also, please remember to post to the list. thanks! >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> On 12/10/2013 02:30 PM, Jon Wieser wrote: >>>>>>>> FS version 5.3 >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wie...@uwm.edu>, Freesurfer@nmr.mgh.harvard.edu >>>>>>>> Sent: Tuesday, December 10, 2013 1:05:26 PM >>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>> >>>>>>>> >>>>>>>> hmmm, it should be there. What version of FS are you using? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>>>>>>>> i was getting the values for the command terminal, when I press the >>>>>>>>> "find clusters and GOTo Max" button on the qdec GUI. >>>>>>>>> there is no file named cache.th20.abs.y.dat or something similar. i >>>>>>>>> did a "find" command to list all the *abs*.dat files in the directory >>>>>>>>> >>>>>>>>> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>>> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >>>>>>>>> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >>>>>>>>> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >>>>>>>>> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>>> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>>> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> these files contain: >>>>>>>>> >>>>>>>>> # CSD PDF/CDF >>>>>>>>> # simtype null-z >>>>>>>>> # anattype surface fsaverage lh >>>>>>>>> # FixGroupSubjectArea 1 >>>>>>>>> # merged 0 >>>>>>>>> # contrast NA >>>>>>>>> # seed 1271277527 >>>>>>>>> # thresh 1.300000 >>>>>>>>> # threshsign 0.000000 >>>>>>>>> # searchspace 74612.965197 >>>>>>>>> # nullfwhm 15.000000 >>>>>>>>> # varfwhm -1.000000 >>>>>>>>> # nrepetitions 10000 >>>>>>>>> # NOTE: nreps and nrepetitions are both valid for volume data. >>>>>>>>> # NOTE: nreps is invalid (-1) for surface data to assure. >>>>>>>>> # NOTE: backwards INcompatibility. >>>>>>>>> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >>>>>>>>> # nreps -1 >>>>>>>>> # FixSurfClusterArea 1 >>>>>>>>> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >>>>>>>>> # nbins 100 >>>>>>>>> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin >>>>>>>>> MaxSigPDF MaxSigCDF >>>>>>>>> 0 204.826004 0.000500 0.999500 0.998289 >>>>>>>>> 2.456050 0.000500 0.999500 >>>>>>>>> 1 220.348267 0.001800 0.997700 0.996805 >>>>>>>>> 2.811329 0.008100 0.991400 >>>>>>>>> 2 235.870529 0.004300 0.993400 0.994388 >>>>>>>>> 3.166609 0.022200 0.969200 >>>>>>>>> 3 251.392792 0.007100 0.986300 0.990673 >>>>>>>>> 3.521888 0.030300 0.938900 >>>>>>>>> 4 266.915039 0.015600 0.970700 0.985251 >>>>>>>>> 3.877167 0.028900 0.910000 >>>>>>>>> 5 282.437317 0.017500 0.953200 0.977702 >>>>>>>>> 4.232447 0.022600 0.887400 >>>>>>>>> 6 297.959595 0.021400 0.931800 0.967628 >>>>>>>>> 4.587726 0.015200 0.872200 >>>>>>>>> 7 313.481842 0.033600 0.898200 0.954689 >>>>>>>>> 4.943005 0.012300 0.859900 >>>>>>>>> 8 329.004089 0.036100 0.862100 0.938634 >>>>>>>>> 5.298285 0.009800 0.850100 >>>>>>>>> 9 344.526367 0.038000 0.824100 0.919325 >>>>>>>>> 5.653563 0.007300 0.842800 >>>>>>>>> 10 360.048645 0.042500 0.781600 0.896747 >>>>>>>>> 6.008843 0.009200 0.833600 >>>>>>>>> 11 375.570892 0.050000 0.731600 0.871009 >>>>>>>>> 6.364122 0.006900 0.826700 >>>>>>>>> 12 391.093140 0.043400 0.688200 0.842332 >>>>>>>>> 6.719401 0.007100 0.819600 >>>>>>>>> 13 406.615417 0.047300 0.640900 0.811034 >>>>>>>>> 7.074681 0.005500 0.814100 >>>>>>>>> 14 422.137695 0.050700 0.590200 0.777508 >>>>>>>>> 7.429960 0.005500 0.808600 >>>>>>>>> 15 437.659943 0.047400 0.542800 0.742195 >>>>>>>>> 7.785239 0.005200 0.803400 >>>>>>>>> 16 453.182190 0.044100 0.498700 0.705560 >>>>>>>>> 8.140518 0.004900 0.798500 >>>>>>>>> 17 468.704468 0.042700 0.456000 0.668070 >>>>>>>>> 8.495798 0.005100 0.793400 >>>>>>>>> 18 484.226746 0.040600 0.415400 0.630176 >>>>>>>>> 8.851077 0.006100 0.787300 >>>>>>>>> 19 499.748962 0.034900 0.380500 0.592300 >>>>>>>>> 9.206356 0.004800 0.782500 >>>>>>>>> 20 515.271240 0.032200 0.348300 0.554820 >>>>>>>>> 9.561636 0.003600 0.778900 >>>>>>>>> 21 530.793518 0.031400 0.316900 0.518067 >>>>>>>>> 9.916915 0.003400 0.775500 >>>>>>>>> 22 546.315796 0.032400 0.284500 0.482320 >>>>>>>>> 10.272194 0.004000 0.771500 >>>>>>>>> 23 561.838013 0.023800 0.260700 0.447809 >>>>>>>>> 10.627474 0.004800 0.766700 >>>>>>>>> 24 577.360291 0.026100 0.234600 0.414711 >>>>>>>>> 10.982753 0.004500 0.762200 >>>>>>>>> 25 592.882568 0.022700 0.211900 0.383160 >>>>>>>>> 11.338033 0.003300 0.758900 >>>>>>>>> 26 608.404846 0.017500 0.194400 0.353244 >>>>>>>>> 11.693312 0.003100 0.755800 >>>>>>>>> 27 623.927063 0.018200 0.176200 0.325018 >>>>>>>>> 12.048591 0.003700 0.752100 >>>>>>>>> 28 639.449341 0.017400 0.158800 0.298504 >>>>>>>>> 12.403871 0.003800 0.748300 >>>>>>>>> 29 654.971619 0.014900 0.143900 0.273697 >>>>>>>>> 12.759150 0.004400 0.743900 >>>>>>>>> 30 670.493896 0.014200 0.129700 0.250569 >>>>>>>>> 13.114429 0.003700 0.740200 >>>>>>>>> 31 686.016113 0.014300 0.115400 0.229078 >>>>>>>>> 13.469708 0.002800 0.737400 >>>>>>>>> 32 701.538391 0.013100 0.102300 0.209165 >>>>>>>>> 13.824987 0.003800 0.733600 >>>>>>>>> 33 717.060669 0.011700 0.090600 0.190763 >>>>>>>>> 14.180266 0.003700 0.729900 >>>>>>>>> 34 732.582947 0.008500 0.082100 0.173798 >>>>>>>>> 14.535546 0.002900 0.727000 >>>>>>>>> 35 748.105164 0.008400 0.073700 0.158191 >>>>>>>>> 14.890825 0.003200 0.723800 >>>>>>>>> 36 763.627441 0.006800 0.066900 0.143861 >>>>>>>>> 15.246104 0.003300 0.720500 >>>>>>>>> 37 779.149719 0.007100 0.059800 0.130727 >>>>>>>>> 15.601384 0.004600 0.715900 >>>>>>>>> 38 794.671936 0.007200 0.052600 0.118707 >>>>>>>>> 15.956663 0.000000 0.715900 >>>>>>>>> 39 810.194214 0.005400 0.047200 0.107723 >>>>>>>>> 16.311943 0.000000 0.715900 >>>>>>>>> 40 825.716492 0.005400 0.041800 0.097698 >>>>>>>>> 16.667221 0.000000 0.715900 >>>>>>>>> 41 841.238770 0.004800 0.037000 0.088559 >>>>>>>>> 17.022501 0.000000 0.715900 >>>>>>>>> 42 856.761047 0.004600 0.032400 0.080237 >>>>>>>>> 17.377781 0.000000 0.715900 >>>>>>>>> 43 872.283264 0.003200 0.029200 0.072665 >>>>>>>>> 17.733059 0.000000 0.715900 >>>>>>>>> 44 887.805542 0.003400 0.025800 0.065783 >>>>>>>>> 18.088339 0.000000 0.715900 >>>>>>>>> 45 903.327820 0.002200 0.023600 0.059531 >>>>>>>>> 18.443619 0.000000 0.715900 >>>>>>>>> 46 918.850037 0.002600 0.021000 0.053855 >>>>>>>>> 18.798897 0.000000 0.715900 >>>>>>>>> 47 934.372314 0.002200 0.018800 0.048707 >>>>>>>>> 19.154179 0.000000 0.715900 >>>>>>>>> 48 949.894592 0.001900 0.016900 0.044040 >>>>>>>>> 19.509457 0.000000 0.715900 >>>>>>>>> 49 965.416870 0.002200 0.014700 0.039810 >>>>>>>>> 19.864735 0.000000 0.715900 >>>>>>>>> 50 980.939148 0.000700 0.014000 0.035979 >>>>>>>>> 20.220016 0.000000 0.715900 >>>>>>>>> 51 996.461365 0.002100 0.011900 0.032510 >>>>>>>>> 20.575294 0.000000 0.715900 >>>>>>>>> 52 1011.983643 0.000800 0.011100 0.029371 >>>>>>>>> 20.930573 0.000000 0.715900 >>>>>>>>> 53 1027.505981 0.000800 0.010300 0.026530 >>>>>>>>> 21.285854 0.000000 0.715900 >>>>>>>>> 54 1043.028198 0.001000 0.009300 0.023961 >>>>>>>>> 21.641132 0.000000 0.715900 >>>>>>>>> 55 1058.550415 0.001000 0.008300 0.021638 >>>>>>>>> 21.996410 0.000000 0.715900 >>>>>>>>> 56 1074.072754 0.000900 0.007400 0.019538 >>>>>>>>> 22.351692 0.000000 0.715900 >>>>>>>>> 57 1089.594971 0.000900 0.006500 0.017640 >>>>>>>>> 22.706970 0.000000 0.715900 >>>>>>>>> 58 1105.117310 0.000800 0.005700 0.015925 >>>>>>>>> 23.062248 0.000000 0.715900 >>>>>>>>> 59 1120.639526 0.000100 0.005600 0.014375 >>>>>>>>> 23.417530 0.000000 0.715900 >>>>>>>>> 60 1136.161743 0.000300 0.005300 0.012975 >>>>>>>>> 23.772808 0.000000 0.715900 >>>>>>>>> 61 1151.684082 0.000800 0.004500 0.011711 >>>>>>>>> 24.128086 0.000000 0.715900 >>>>>>>>> 62 1167.206299 0.000400 0.004100 0.010569 >>>>>>>>> 24.483368 0.000000 0.715900 >>>>>>>>> 63 1182.728516 0.000200 0.003900 0.009538 >>>>>>>>> 24.838646 0.000000 0.715900 >>>>>>>>> 64 1198.250854 0.000200 0.003700 0.008607 >>>>>>>>> 25.193924 0.000000 0.715900 >>>>>>>>> 65 1213.773071 0.000300 0.003400 0.007767 >>>>>>>>> 25.549206 0.000000 0.715900 >>>>>>>>> 66 1229.295410 0.000400 0.003000 0.007008 >>>>>>>>> 25.904484 0.000000 0.715900 >>>>>>>>> 67 1244.817627 0.000400 0.002600 0.006323 >>>>>>>>> 26.259762 0.000000 0.715900 >>>>>>>>> 68 1260.339966 0.000300 0.002300 0.005705 >>>>>>>>> 26.615044 0.000000 0.715900 >>>>>>>>> 69 1275.862183 0.000400 0.001900 0.005147 >>>>>>>>> 26.970322 0.000000 0.715900 >>>>>>>>> 70 1291.384399 0.000100 0.001800 0.004644 >>>>>>>>> 27.325600 0.000000 0.715900 >>>>>>>>> 71 1306.906738 0.000000 0.001800 0.004190 >>>>>>>>> 27.680882 0.000000 0.715900 >>>>>>>>> 72 1322.428955 0.000400 0.001400 0.003780 >>>>>>>>> 28.036160 0.000000 0.715900 >>>>>>>>> 73 1337.951172 0.000100 0.001300 0.003410 >>>>>>>>> 28.391438 0.000000 0.715900 >>>>>>>>> 74 1353.473511 0.000100 0.001200 0.003076 >>>>>>>>> 28.746719 0.000000 0.715900 >>>>>>>>> 75 1368.995728 0.000100 0.001100 0.002775 >>>>>>>>> 29.101997 0.000000 0.715900 >>>>>>>>> 76 1384.517944 0.000100 0.001000 0.002503 >>>>>>>>> 29.457275 0.000000 0.715900 >>>>>>>>> 77 1400.040283 0.000300 0.000700 0.002258 >>>>>>>>> 29.812557 0.000000 0.715900 >>>>>>>>> 78 1415.562500 0.000100 0.000600 0.002037 >>>>>>>>> 30.167835 0.000000 0.715900 >>>>>>>>> 79 1431.084839 0.000000 0.000600 0.001838 >>>>>>>>> 30.523113 0.000000 0.715900 >>>>>>>>> 80 1446.607056 0.000100 0.000500 0.001658 >>>>>>>>> 30.878395 0.000000 0.715900 >>>>>>>>> 81 1462.129272 0.000200 0.000300 0.001495 >>>>>>>>> 31.233673 0.000000 0.715900 >>>>>>>>> 82 1477.651611 0.000000 0.000300 0.001349 >>>>>>>>> 31.588951 0.000000 0.715900 >>>>>>>>> 83 1493.173828 0.000200 0.000100 0.001217 >>>>>>>>> 31.944233 0.000000 0.715900 >>>>>>>>> 84 1508.696167 0.000000 0.000100 0.001098 >>>>>>>>> 32.299511 0.000000 0.715900 >>>>>>>>> 85 1524.218384 0.000000 0.000100 0.000990 >>>>>>>>> 32.654789 0.000000 0.715900 >>>>>>>>> 86 1539.740601 0.000000 0.000100 0.000893 >>>>>>>>> 33.010071 0.000000 0.715900 >>>>>>>>> 87 1555.262939 0.000000 0.000100 0.000805 >>>>>>>>> 33.365349 0.000000 0.715900 >>>>>>>>> 88 1570.785156 0.000000 0.000100 0.000727 >>>>>>>>> 33.720627 0.000000 0.715900 >>>>>>>>> 89 1586.307373 0.000000 0.000100 0.000655 >>>>>>>>> 34.075909 0.000000 0.715900 >>>>>>>>> 90 1601.829712 0.000000 0.000100 0.000591 >>>>>>>>> 34.431187 0.000000 0.715900 >>>>>>>>> 91 1617.351929 0.000000 0.000100 0.000533 >>>>>>>>> 34.786469 0.000000 0.715900 >>>>>>>>> 92 1632.874146 0.000000 0.000100 0.000481 >>>>>>>>> 35.141747 0.000000 0.715900 >>>>>>>>> 93 1648.396484 0.000000 0.000100 0.000434 >>>>>>>>> 35.497025 0.000000 0.715900 >>>>>>>>> 94 1663.918701 0.000000 0.000100 0.000391 >>>>>>>>> 35.852306 0.000000 0.715900 >>>>>>>>> 95 1679.441040 0.000000 0.000100 0.000353 >>>>>>>>> 36.207584 0.000000 0.715900 >>>>>>>>> 96 1694.963257 0.000000 0.000100 0.000318 >>>>>>>>> 36.562862 0.000000 0.715900 >>>>>>>>> 97 1710.485474 0.000000 0.000100 0.000287 >>>>>>>>> 36.918144 0.000000 0.715900 >>>>>>>>> 98 1726.007812 0.000000 0.000100 0.000259 >>>>>>>>> 37.273422 0.000000 0.715900 >>>>>>>>> 99 1741.530029 0.000100 -0.000000 0.000234 >>>>>>>>> 37.628700 0.715900 0.000000 >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>>> To: "Jon Wieser" <wie...@uwm.edu> >>>>>>>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> Sent: Monday, December 9, 2013 5:02:41 PM >>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>> >>>>>>>>> which file did you look in? It should have a name like >>>>>>>>> cache.th20.abs.y.ocn.dat >>>>>>>>> >>>>>>>>> On 12/09/2013 05:09 PM, Jon Wieser wrote: >>>>>>>>>> I found data for the average thickness all subjects for each >>>>>>>>>> cluster, but I haven't found the individual subject's thickness for >>>>>>>>>> each cluster. can you direct me to that data? >>>>>>>>>> Jon >>>>>>>>>> ----- Original Message ----- >>>>>>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>>>> To: "Jon Wieser" <wie...@uwm.edu> >>>>>>>>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> Sent: Monday, December 9, 2013 2:15:39 PM >>>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>>> >>>>>>>>>> It is in one of the output files. Look for the .dat file in >>>>>>>>>> mri_glmfit-sim --help >>>>>>>>>> >>>>>>>>>> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>>>>>>>>>> thanks doug, >>>>>>>>>>> >>>>>>>>>>> We've run a 2x2 analysis for thickness in Qdec and want the get >>>>>>>>>>> the average thickness value for each cluster, for each subject. >>>>>>>>>>> How can i get a table of thickness data , for feach subject in the >>>>>>>>>>> analysis >>>>>>>>>>> Jon >>>>>>>>>>> >>>>>>>>>>> ----- Original Message ----- >>>>>>>>>>> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>>>>>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>>>>> >>>>>>>>>>> doug >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>>>>> HI freesurfer experts >>>>>>>>>>>> >>>>>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana >>>>>>>>>>>> usage) and 2 covariates(age and gender) to study the effect of >>>>>>>>>>>> these factors on cortical thickness. I can only select a covariate >>>>>>>>>>>> in the qdec gui. is there a way to select both covariates in the >>>>>>>>>>>> qdec GUI? >>>>>>>>>>>> Thanks >>>>>>>>>>>> Jon >>>>>>>>>>>> -- 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/ 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
