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. 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$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Studies/IDEAA_grant/MTA cmdline mri_glmfit --y /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/y.mgh --fsgd /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/qdec.fsgd dods --glmdir /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset --surf fsaverage lh --label /Studies/IDEAA_grant/MTA/fsaverage/label/lh.aparc.label --C /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/contrasts/lh-Avg-Intercept-thickness.mat --C /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/contrasts/lh-Diff-EO_0-EO_1-Intercept-thickness.mat --C /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/contrasts/lh-Diff-ADHD-nonADHD-Intercept-thickness.mat --C /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/contrasts/lh-X-MJ_earlyonset-ADHD_group-Intercept-thickness.mat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/y.mgh logyflag 0 usedti 0 FSGD /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset/qdec.fsgd labelmask /Studies/IDEAA_grant/MTA/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Studies/IDEAA_grant/MTA/qdec/MJ_ADHD_age_onset IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM 14.517652 SearchSpace 73649.347769 anattype surface
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