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 data similar to that represented in the scatter plot but for the average of the cluster, not just one vertex, for all of the 45 clusters, values of thickness for each subject. is that possible? I tried running 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 >>>>
