I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>
look at the CWP column doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --simERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>>
so in the following cluster, the cluster-wise p-value is 0.80130?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.247 90900 134.66 -37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 16, 2013 4:28:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --simERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>>
Yes, with a 95% confidence range of .7962 to .8065 doug
On 12/17/2013 11:04 AM, Jon Wieser wrote:
so in the following cluster, the cluster-wise p-value is 0.80130?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.247 90900 134.66 -37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 16, 2013 4:28:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --simERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>>>
I would think that a p-value of 0.8013 is very insignificant. Am I missing somthing? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 17, 2013 10:46:36 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
Yes, with a 95% confidence range of .7962 to .8065 doug
On 12/17/2013 11:04 AM, Jon Wieser wrote:
so in the following cluster, the cluster-wise p-value is 0.80130?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.247 90900 134.66 -37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 16, 2013 4:28:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --simERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>>>
Yes, it is insignificant. I had you set the clusterwise p-value threshold (--cwp) to .99999 which means keep all the clusters regardless of how significant it is because you wanted the 40 clusters.
On 12/17/2013 12:21 PM, Jon Wieser wrote:
I would think that a p-value of 0.8013 is very insignificant. Am I missing somthing? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 17, 2013 10:46:36 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
Yes, with a 95% confidence range of .7962 to .8065 doug
On 12/17/2013 11:04 AM, Jon Wieser wrote:
so in the following cluster, the cluster-wise p-value is 0.80130?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.247 90900 134.66 -37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 16, 2013 4:28:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
Hi Doug
I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .999999999
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try something like --cwp .999999999
On 12/13/2013 01:03 PM, Jon Wieser wrote:
HI doug thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. perhaps theses are the most significant clusters? Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:43:29 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
use the command I gave you before just add --cwp .99 to it doug
On 12/13/2013 12:25 PM, Jon Wieser wrote:
Hi doug it's requesting the --sim option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99ERROR: must spec --sim
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --simERROR: flag --sim requires four arguments
what args do I give the --sim!
Jon
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>>> To: "Jon Wieser" wieser@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" greve@nmr.mgh.harvard.edu >>>>>>>>> To: "Jon Wieser" wieser@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" greve@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 >>>>>>>>>>>
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jon Wieser