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 >>>>>>>> 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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
