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/ _______________________________________________ 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.
