Is it possible to get the individual subject data for the clusters, before the monte carlo simulation has been run? I click "find clusters and goto max" . then on the command line it shows me the clusters stats and then when I click the "next" button under "Clusters". it shows me the graph of the thickness for each cluster, with thickness values for all subjects. is it possible to output the data values used to make the graph? Jon
----- Original Message ----- From: "Jon Wieser" <wie...@uwm.edu> To: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, December 10, 2013 4:32:10 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates 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 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
