Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

funcroi commands
by Emily Boeke 13 Dec '13

13 Dec '13

Hi Freesurfers, I would like to make sure I am using the funcroi commands correctly for anatomical and functional ROI analyses (using the aseg to anatomically constrain), and I have some questions about the commands. If I want to extract the average percent signal change in the whole left amygdala for a particular contrast, is this the correct version of the commands to run? 1. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> 2. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 3. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -c <contrast> -m cespct If I want to extract the average percent signal change from an anatomically constrained functional ROI (e.g. an ROI representing activation in a certain contrast within the lh amygdala), is this the correct version of the commands to run: 4. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> -contrast <contrast> -sign pos -thresh 1.3 5. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 6. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -a <analysisname> -c <contrast> -m cespct My questions are (regarding the second set of commands): -in the right hippocampus example under funcroi-config --help, the anatomical constraint is specified with --annot aseg.mgz 53, but it should be --seg aseg.mgz 53 like in my examples, correct? Otherwise you get an error. -Is it ok to use one analysis name in the funcroi-config file and another in funcroi-table-sess? Would that allow me to make an ROI from one analysis and use it to extract signal from another analysis? -If I get a message saying some subjects had "empty ROIs" and the value in the table for them is 0, does this mean that subjects had no activation (meeting the threshold specified) in the first contrast I specified (in funcroi-config) so no ROI could be created from their activation? -If I want to look at activation in more than one anatomical region (for example, bilateral amygdala), is there any way to do that with the -seg option? Pardon the long message. Thanks for the help! Emily

2 7

Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 13 Dec '13

13 Dec '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>>>> >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>>>> HI freesurfer experts >>>>>>>>>>> >>>>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>>>> Thanks >>>>>>>>>>> Jon >>>>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 4

.nii file visualization in tkmedit
by Garikoitz Lerma-Usabiaga 13 Dec '13

13 Dec '13

Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly in mricron and tkmedit with the following command: tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay MEG_ROI.nii -fthresh 0.5 (single_subj_T1.nii is Colin27) but when I visualize it with: tkmedit Colin T1.mgz -overlay ./rC_vs_D_band1_0.01_left.nii -overlay-reg /home/glerma/glerma/GIT/bcblscripts/FREESURFER/ROI/Mikel_SingleSubject_to_Colin.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white The result is wrong, and different from the first tkmedit. Should I convert the MEG_ROI.nii ni some specific way to make it work? Any suggestions? Thanks, Gari The registration matrix between single_subj_T1.nii and Colin27 is the following one: Colin 2.000000 2.000000 0.150000 9.999982714653015e-01 -1.096551306545734e-03 -1.517703873105347e-03 5.575752854347229e-01 1.516161020845175e-03 -1.406581024639308e-03 9.999977946281433e-01 -1.579373359680176e+00 -1.098683569580317e-03 -9.999984502792358e-01 -1.404915703460574e-03 6.750410795211792e-01 0 0 0 1 round (obtained with: bbregister --s Colin --mov path/to/spm8/canonical/single_subj_T1.nii --init-spm --reg from_SingleSubject_to_Colin.dat --t1 )

2 5

Fwd: qdec analysis with 2 covariates
by Jon Wieser 12 Dec '13

12 Dec '13

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(a)nmr.mgh.harvard.edu> To: "Jon Wieser" <wieser(a)uwm.edu> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>>> >>>>>>>>> doug >>>>>>>>> >>>>>>>>> >>>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>>> HI freesurfer experts >>>>>>>>>> >>>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>>> Thanks >>>>>>>>>> Jon >>>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 12 Dec '13

12 Dec '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>> >>>>>>>> >>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>> HI freesurfer experts >>>>>>>>> >>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>> Thanks >>>>>>>>> Jon >>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 5

Editing Question -- Isthmus Cingulate
by Luke W. Bonham 12 Dec '13

12 Dec '13

> Hi, > > I'm having trouble figuring out how to correct this error around the > isthmus cingulate (screenshot attached). It's come up several times in the > cohort I'm editing and there's been little success in correcting the pial > boundary. It doesn't seem to be addressable with cp, wm edits, or the > expert options I know of. Any tips are greatly appreciated! > > Thanks >

1 0

Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
by Bruce Fischl 12 Dec '13

12 Dec '13

yes, I think so. Why are you restarting? Or do mean start another one? On Tue, 26 Nov 2013, pablo najt wrote: > Thank you Bruce for your reply.Yes the computed has over 32 GB. > Let me check if I understood. > So far I have been running recon -all in a snow leopard for running as part > of the longitudinal stream. > If I want to re-start with this analysis in the FS 5.3 version for Centos > you are suggesting I can use the a new recon -all command (-openmp 8 flag to > recon-all)? > Thanks. > Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: pablonajt(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > Hi Pablo > > it also depends on how much ram it has. You should be able to run 1 > significantly faster using the -openmp 8 flag to recon-all, or 8 (if you > have enough ram, probably at least 32G) > > cheers > Bruce > > On Tue, 26 Nov 2013, pablo najt > wrote: > > > Dear Bruce,Last week I emailed with the question of how many recon -all > > separate subjects I could run in parallel with the FS version 5.3 for Cent > os > > 6. You answered that this depends on how many cores my machine has. > > I just found out that our workstation has two processors with 4 cores each > > (8 cores in total). > > Would you be able to tell me how many subjects could I run in parallel wit > h > > our workstation? > > Thank you for your support, > > Pablo > > > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > > From: fischl(a)nmr.mgh.harvard.edu > > To: pablonajt(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > Hi Pablo > > > > it depends on how many cores you have > > > > Bruce > > On Thu, 21 Nov 2013, pablo najt wrote: > > > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I > a > > m > > > wondering up to how many recon -all for separate subjects I can run in > > > parallel. With the version of Snow Leopard 32b I was running two at a ti > me > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > el > > ? > > > If so would this process still efficient or there is an optimum number? > > > Thank you, > > > Pablo > > > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > > From: zkaufman(a)nmr.mgh.harvard.edu > > > > To: garikoitz(a)gmail.com > > > > CC: pablonajt(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > > CentOS 6 > > > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > > CentOS6 build. > > > > > > > > -Zeke > > > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a > ny > > > > > reason to not use this version in your CentOS 6, if you have some ot > he > > r > > > > > requirements maybe Nick or Zeke could help you better, I am just an > us > > er > > > :) > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt(a)hotmail.com > > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > > > Dear Gari, > > > > > Thank you for the advice. One additional question. > > > > > Considering that I will start from scratch the processing in the > > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > > Thanks, > > > > > Pablo > > > > > > > > > > -------------------------------------------------------------------- > -- > > -- > > > > > From: garikoitz(a)gmail.com <mailto:garikoitz@gmail.com> > > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > > To: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > and CentOS 6 > > > > > > > > > > > > > > > Hi Pablo, > > > > > you shouldn't mix different OS-s or software version in the same > > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > > operating system version on anatomical volume and cortical thickness > > > > > measurements. /PloS one/, /7/(6), e38234. > > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > > it works too). > > > > > regards! > > > > > Gari > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt(a)hotmail.com > > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > > > Dear FS experts, > > > > > I am forwarding my question (please see below), in case it got > > > > > lost among the intense flow of messages. > > > > > Thank you for your consideration. > > > > > Pablo > > > > > > > > > > -------------------------------------------------------------------- > -- > > -- > > > > > From: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > Date: Mon, 18 Nov 2013 16:38:41 +0000 > > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > and CentOS 6 > > > > > > > > > > > > > > > Dear FS experts, > > > > > I have a question about compatibility for running recon-all > > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > > wondering if I could process additional subjects in parallel > > > > > with this other machine that are also intended to be included in > > > > > the longitudinal stream. > > > > > Also, I am not sure about whether I should be installing in the > > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > > because of compatibility issues. > > > > > Thank you very much for your attention, > > > > > Pablo > > > > > > > > > > > > > > > _______________________________________________ Freesurfer > > > > > mailing list Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > > > > > information in this e-mail is intended only for the person to > > > > > whom it is addressed. If you believe this e-mail was sent to you > > > > > in error and the e-mail contains patient information, please > > > > > contact the Partners Compliance HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent > > > > > to you in error but does not contain patient information, please > > > > > contact the sender and properly dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person > > > > > to whom it is > > > > > addressed. If you believe this e-mail was sent to you in error > > > > > and the e-mail > > > > > contains patient information, please contact the Partners > > > > > Compliance HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent > > > > > to you in error > > > > > but does not contain patient information, please contact the > > > > > sender and properly > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing > > > > > list Freesurfer(a)nmr.mgh.harvard.edu > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > > > > > information in this e-mail is intended only for the person to whom > > > > > it is addressed. If you believe this e-mail was sent to you in error > > > > > and the e-mail contains patient information, please contact the > > > > > Partners Compliance HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > > > you in error but does not contain patient information, please > > > > > contact the sender and properly dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.ed > u> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > whom it is > > > > > addressed. If you believe this e-mail was sent to you in error and > > > > > the e-mail > > > > > contains patient information, please contact the Partners Compliance > > > > > HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > > > you in error > > > > > but does not contain patient information, please contact the sender > > > > > and properly > > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati > on > > in this e-mail is intended only for the person to whom it is addressed. If > > you believe this e-mail was sent to you in error and the e-mail contains > > patient information, please contact the Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error but does not contain patient information, please contact the sender > > and properly dispose of the e-mail. > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information > in this e-mail is intended only for the person to whom it is addressed. If > you believe this e-mail was sent to you in error and the e-mail contains > patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender > and properly dispose of the e-mail. > >

2 2

after editing pial boundary in tkmedit
by Rujing Zha 12 Dec '13

12 Dec '13

Hi Doug and Bruce, I have run "recon-all -autorecon-pial -s my_subject" after editing the pial by tkmedit. I donot know wether "-autorecon-pial" option running the process stages 24-31. So I want to know wether I need run "-autorecon3" option as I run "-autorecon-pial" not "-autorecon2-pial" previously. Can I ensure 24-31 steps being done by running the "recon-all -autorecon3 -s my_subject". GM thickness group analysis should be done correctly. Thanks. All the best. 2013-12-12 Rujing Zha

1 0

Tracula error ? set: Variable name must begin with a letter
by Matthieu Vanhoutte 12 Dec '13

12 Dec '13

Hello experts, I am running the first pre-processing step in Tracula on FS 5.1 and come across the error: *set: Variable name must begin with a letter* I have attached my dmrirc file. Did I make a mistake in this file? Best regards, Matthieu

2 4

Freesurfer versions
by Erik Lindberg 12 Dec '13

12 Dec '13

Dear Freesurfer experts, I am attaching a document showing the segmentation of a brain in version 5.1 and 5.3 with and without a 3-T flag. Image is from a 3-T camera. What I am wondering about is that it seems that the cortex is too thin in the later version of Freesurfer (both when using 3T flag and when not using this flag). Is there some other flag that could be used to deal with this? Thanks Olof Erik

1 0

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