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
