It is hard to say, since 4.5 came out 3 years ago:). It is ok to do group analysis in a different version of FS. doug ps. Please remember to copy the list instead of sending emails directly to us. thanks!
On 07/02/2013 01:53 PM, Emily Boeke wrote: > Strange, I have run simulations before in 4.5 and gotten talairach coords. > Are you sure there isn't any other reason the coordinates are in this format > in this simulation? > > Is it generally ok to do a group analysis in a later version of freesurfer if > the first level analyses have been done in 4.5? Or would you recommend > redoing the individual analyses as well? > > Thanks! > Emily > > On Jul 2, 2013, at 12:18 PM, Douglas N Greve wrote: > >> OK, in later versions it will give you the talairach coords. I would >> download 5.3 and run your group analysis in that, just be careful not to >> run recon-all using 5.3 (unless you want to upgrade all your subjects). >> doug >> >> On 07/02/2013 11:48 AM, Emily Boeke wrote: >>> 4.5 >>> >>> Emily >>> On Jul 2, 2013, at 11:45 AM, Douglas N Greve wrote: >>> >>>> Hi Emily, what version of FS are you using? >>>> doug >>>> >>>> >>>> On 07/02/2013 11:41 AM, Emily Boeke wrote: >>>>> Hi Doug, >>>>> >>>>> Sorry to be overly persistent, but I just wanted to make sure you saw >>>>> this email! >>>>> >>>>> Thanks, >>>>> Emily >>>>> >>>>> On Jul 1, 2013, at 9:20 AM, Emily Boeke wrote: >>>>> >>>>>> This was the command I ran: >>>>>> >>>>>> mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 10000 2 >>>>>> HvL.SBQ.2.10000.pos --stim-sign pos >>>>>> >>>>>> On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote: >>>>>> >>>>>>> Hi Emily, what is your mri_glmfit-sim command line? >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> On 06/28/2013 02:40 PM, Emily Boeke wrote: >>>>>>>> Any thoughts on why this file turned out this way? >>>>>>>> >>>>>>>> Thanks! >>>>>>>> Emily >>>>>>>> >>>>>>>> On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote: >>>>>>>> >>>>>>>>> Sure, here it is: >>>>>>>>> >>>>>>>>> # Cluster Growing Summary (mri_volcluster) >>>>>>>>> # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ >>>>>>>>> # cwd >>>>>>>>> /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car >>>>>>>>> # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd >>>>>>>>> tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask >>>>>>>>> tal.sm.wls.pct.rfx//mask.mgh --cwsig >>>>>>>>> tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig >>>>>>>>> tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum >>>>>>>>> tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn >>>>>>>>> tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf >>>>>>>>> tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat >>>>>>>>> # sysname Linux >>>>>>>>> # hostname compute-0-114 >>>>>>>>> # machine x86_64 >>>>>>>>> # user eboeke01 >>>>>>>>> # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh >>>>>>>>> # Frame Number: 0 >>>>>>>>> # Minimum Threshold: 2 >>>>>>>>> # Maximum Threshold: inifinity >>>>>>>>> # Threshold Sign: pos >>>>>>>>> # AdjustThreshWhenOneTail 1 >>>>>>>>> # Size Threshold: 0 mm^3 >>>>>>>>> # Size Threshold: 0 voxels >>>>>>>>> # Voxel Size: 8 mm^3 >>>>>>>>> # Registration: None : Tal Coords invalid >>>>>>>>> # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh >>>>>>>>> # Mask Thresh: 0.500000 >>>>>>>>> # Mask Sign: abs >>>>>>>>> # Mask Invert: 0 >>>>>>>>> # AllowDiag: 0 >>>>>>>>> # NClusters 192 >>>>>>>>> # CSD thresh 2.000000 >>>>>>>>> # CSD nreps 10000 >>>>>>>>> # CSD simtype mc-z >>>>>>>>> # CSD contrast group >>>>>>>>> # CSD confint 90.000000 >>>>>>>>> # >>>>>>>>> # Reporting Coordinates in Voxel Indices >>>>>>>>> # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ >>>>>>>>> Max# CWP CWPLow CWPHi >>>>>>>>> 1 597 4776.0 30.00 50.00 65.00 >>>>>>>>> 5.94673 0.02490 0.02290 0.02690 >>>>>>>>> 2 730 5840.0 27.00 28.00 86.00 >>>>>>>>> 5.56628 0.00720 0.00610 0.00830 >>>>>>>>> 3 1124 8992.0 5.00 18.00 38.00 >>>>>>>>> 5.01850 0.00010 0.00000 0.00020 >>>>>>>>> 4 259 2072.0 59.00 20.00 78.00 >>>>>>>>> 5.01465 0.68360 0.67760 0.68960 >>>>>>>>> 5 279 2232.0 18.00 22.00 73.00 >>>>>>>>> 3.94952 0.58840 0.58210 0.59470 >>>>>>>>> 6 194 1552.0 35.00 66.00 76.00 >>>>>>>>> 3.94297 0.93630 0.93320 0.93940 >>>>>>>>> 7 664 5312.0 32.00 15.00 60.00 >>>>>>>>> 3.68551 0.01400 0.01250 0.01550 >>>>>>>>> 8 293 2344.0 28.00 5.00 58.00 >>>>>>>>> 3.66686 0.52560 0.51920 0.53200 >>>>>>>>> 9 49 392.0 12.00 52.00 58.00 >>>>>>>>> 3.63351 1.00000 -0.00010 1.00000 >>>>>>>>> 10 150 1200.0 5.00 4.00 28.00 >>>>>>>>> 3.62637 0.99560 0.99470 0.99640 >>>>>>>>> 11 298 2384.0 12.00 47.00 86.00 >>>>>>>>> 3.58250 0.50260 0.49620 0.50900 >>>>>>>>> 12 343 2744.0 13.00 39.00 60.00 >>>>>>>>> 3.57829 0.33900 0.33290 0.34510 >>>>>>>>> 13 467 3736.0 21.00 42.00 49.00 >>>>>>>>> 3.53307 0.09590 0.09210 0.09970 >>>>>>>>> 14 276 2208.0 49.00 36.00 56.00 >>>>>>>>> 3.51549 0.60280 0.59650 0.60910 >>>>>>>>> 15 134 1072.0 70.00 17.00 34.00 >>>>>>>>> 3.38623 0.99890 0.99850 0.99930 >>>>>>>>> 16 75 600.0 5.00 25.00 55.00 >>>>>>>>> 3.09334 1.00000 -0.00010 1.00000 >>>>>>>>> 17 74 592.0 13.00 10.00 49.00 >>>>>>>>> 3.03017 1.00000 -0.00010 1.00000 >>>>>>>>> 18 45 360.0 65.00 39.00 62.00 >>>>>>>>> 3.00205 1.00000 -0.00010 1.00000 >>>>>>>>> 19 15 120.0 72.00 7.00 42.00 >>>>>>>>> 2.96283 1.00000 -0.00010 1.00000 >>>>>>>>> 20 55 440.0 62.00 9.00 23.00 >>>>>>>>> 2.93121 1.00000 -0.00010 1.00000 >>>>>>>>> 21 79 632.0 46.00 60.00 87.00 >>>>>>>>> 2.92199 1.00000 -0.00010 1.00000 >>>>>>>>> 22 35 280.0 2.00 41.00 48.00 >>>>>>>>> 2.84065 1.00000 -0.00010 1.00000 >>>>>>>>> 23 44 352.0 6.00 35.00 27.00 >>>>>>>>> 2.80109 1.00000 -0.00010 1.00000 >>>>>>>>> 24 14 112.0 50.00 3.00 54.00 >>>>>>>>> 2.75399 1.00000 -0.00010 1.00000 >>>>>>>>> 25 71 568.0 0.00 22.00 9.00 >>>>>>>>> 2.75160 1.00000 -0.00010 1.00000 >>>>>>>>> 26 5 40.0 28.00 0.00 36.00 >>>>>>>>> 2.72535 1.00000 -0.00010 1.00000 >>>>>>>>> 27 130 1040.0 40.00 1.00 45.00 >>>>>>>>> 2.71826 0.99920 0.99880 0.99950 >>>>>>>>> 28 81 648.0 33.00 61.00 86.00 >>>>>>>>> 2.70040 1.00000 -0.00010 1.00000 >>>>>>>>> 29 73 584.0 67.00 26.00 52.00 >>>>>>>>> 2.68744 1.00000 -0.00010 1.00000 >>>>>>>>> 30 16 128.0 64.00 48.00 72.00 >>>>>>>>> 2.67636 1.00000 -0.00010 1.00000 >>>>>>>>> 31 28 224.0 75.00 35.00 88.00 >>>>>>>>> 2.65193 1.00000 -0.00010 1.00000 >>>>>>>>> 32 11 88.0 15.00 21.00 82.00 >>>>>>>>> 2.61771 1.00000 -0.00010 1.00000 >>>>>>>>> 33 5 40.0 45.00 0.00 27.00 >>>>>>>>> 2.61424 1.00000 -0.00010 1.00000 >>>>>>>>> 34 16 128.0 9.00 13.00 70.00 >>>>>>>>> 2.58842 1.00000 -0.00010 1.00000 >>>>>>>>> 35 23 184.0 15.00 27.00 48.00 >>>>>>>>> 2.57410 1.00000 -0.00010 1.00000 >>>>>>>>> 36 28 224.0 15.00 31.00 44.00 >>>>>>>>> 2.57219 1.00000 -0.00010 1.00000 >>>>>>>>> 37 23 184.0 29.00 56.00 78.00 >>>>>>>>> 2.55890 1.00000 -0.00010 1.00000 >>>>>>>>> 38 7 56.0 0.00 42.00 92.00 >>>>>>>>> 2.55525 1.00000 -0.00010 1.00000 >>>>>>>>> 39 49 392.0 52.00 40.00 88.00 >>>>>>>>> 2.54894 1.00000 -0.00010 1.00000 >>>>>>>>> 40 42 336.0 7.00 31.00 63.00 >>>>>>>>> 2.52160 1.00000 -0.00010 1.00000 >>>>>>>>> 41 37 296.0 22.00 43.00 81.00 >>>>>>>>> 2.50557 1.00000 -0.00010 1.00000 >>>>>>>>> 42 21 168.0 22.00 58.00 72.00 >>>>>>>>> 2.49912 1.00000 -0.00010 1.00000 >>>>>>>>> 43 32 256.0 59.00 45.00 91.00 >>>>>>>>> 2.44918 1.00000 -0.00010 1.00000 >>>>>>>>> 44 12 96.0 31.00 29.00 36.00 >>>>>>>>> 2.42939 1.00000 -0.00010 1.00000 >>>>>>>>> 45 50 400.0 14.00 34.00 26.00 >>>>>>>>> 2.42102 1.00000 -0.00010 1.00000 >>>>>>>>> 46 22 176.0 6.00 15.00 55.00 >>>>>>>>> 2.41349 1.00000 -0.00010 1.00000 >>>>>>>>> 47 12 96.0 9.00 43.00 42.00 >>>>>>>>> 2.40593 1.00000 -0.00010 1.00000 >>>>>>>>> 48 27 216.0 64.00 17.00 31.00 >>>>>>>>> 2.38351 1.00000 -0.00010 1.00000 >>>>>>>>> 49 16 128.0 25.00 49.00 81.00 >>>>>>>>> 2.37500 1.00000 -0.00010 1.00000 >>>>>>>>> 50 37 296.0 12.00 18.00 54.00 >>>>>>>>> 2.36836 1.00000 -0.00010 1.00000 >>>>>>>>> 51 22 176.0 43.00 50.00 63.00 >>>>>>>>> 2.35072 1.00000 -0.00010 1.00000 >>>>>>>>> 52 39 312.0 31.00 39.00 46.00 >>>>>>>>> 2.31633 1.00000 -0.00010 1.00000 >>>>>>>>> 53 7 56.0 75.00 60.00 84.00 >>>>>>>>> 2.28945 1.00000 -0.00010 1.00000 >>>>>>>>> 54 6 48.0 33.00 25.00 67.00 >>>>>>>>> 2.28154 1.00000 -0.00010 1.00000 >>>>>>>>> 55 10 80.0 49.00 40.00 33.00 >>>>>>>>> 2.27301 1.00000 -0.00010 1.00000 >>>>>>>>> 56 13 104.0 26.00 65.00 88.00 >>>>>>>>> 2.27017 1.00000 -0.00010 1.00000 >>>>>>>>> 57 6 48.0 13.00 25.00 26.00 >>>>>>>>> 2.26583 1.00000 -0.00010 1.00000 >>>>>>>>> 58 15 120.0 54.00 9.00 20.00 >>>>>>>>> 2.25868 1.00000 -0.00010 1.00000 >>>>>>>>> 59 16 128.0 63.00 14.00 19.00 >>>>>>>>> 2.21490 1.00000 -0.00010 1.00000 >>>>>>>>> 60 4 32.0 9.00 25.00 61.00 >>>>>>>>> 2.21056 1.00000 -0.00010 1.00000 >>>>>>>>> 61 37 296.0 25.00 37.00 62.00 >>>>>>>>> 2.21055 1.00000 -0.00010 1.00000 >>>>>>>>> 62 10 80.0 59.00 51.00 51.00 >>>>>>>>> 2.20982 1.00000 -0.00010 1.00000 >>>>>>>>> 63 20 160.0 66.00 41.00 51.00 >>>>>>>>> 2.19863 1.00000 -0.00010 1.00000 >>>>>>>>> 64 2 16.0 53.00 66.00 72.00 >>>>>>>>> 2.18410 1.00000 -0.00010 1.00000 >>>>>>>>> 65 9 72.0 37.00 38.00 66.00 >>>>>>>>> 2.17739 1.00000 -0.00010 1.00000 >>>>>>>>> 66 6 48.0 6.00 44.00 62.00 >>>>>>>>> 2.17461 1.00000 -0.00010 1.00000 >>>>>>>>> 67 39 312.0 50.00 35.00 70.00 >>>>>>>>> 2.16322 1.00000 -0.00010 1.00000 >>>>>>>>> 68 11 88.0 52.00 6.00 21.00 >>>>>>>>> 2.16002 1.00000 -0.00010 1.00000 >>>>>>>>> 69 6 48.0 26.00 0.00 43.00 >>>>>>>>> 2.15030 1.00000 -0.00010 1.00000 >>>>>>>>> 70 8 64.0 41.00 16.00 19.00 >>>>>>>>> 2.14875 1.00000 -0.00010 1.00000 >>>>>>>>> 71 4 32.0 51.00 8.00 39.00 >>>>>>>>> 2.14592 1.00000 -0.00010 1.00000 >>>>>>>>> 72 3 24.0 47.00 9.00 21.00 >>>>>>>>> 2.14285 1.00000 -0.00010 1.00000 >>>>>>>>> 73 8 64.0 67.00 19.00 27.00 >>>>>>>>> 2.14034 1.00000 -0.00010 1.00000 >>>>>>>>> 74 12 96.0 3.00 59.00 86.00 >>>>>>>>> 2.13879 1.00000 -0.00010 1.00000 >>>>>>>>> 75 3 24.0 15.00 6.00 19.00 >>>>>>>>> 2.13024 1.00000 -0.00010 1.00000 >>>>>>>>> 76 9 72.0 59.00 41.00 41.00 >>>>>>>>> 2.12204 1.00000 -0.00010 1.00000 >>>>>>>>> 77 18 144.0 35.00 48.00 55.00 >>>>>>>>> 2.10334 1.00000 -0.00010 1.00000 >>>>>>>>> 78 6 48.0 40.00 57.00 92.00 >>>>>>>>> 2.08841 1.00000 -0.00010 1.00000 >>>>>>>>> 79 7 56.0 43.00 1.00 17.00 >>>>>>>>> 2.07371 1.00000 -0.00010 1.00000 >>>>>>>>> 80 6 48.0 41.00 55.00 69.00 >>>>>>>>> 2.07007 1.00000 -0.00010 1.00000 >>>>>>>>> 81 14 112.0 23.00 35.00 88.00 >>>>>>>>> 2.06307 1.00000 -0.00010 1.00000 >>>>>>>>> 82 11 88.0 40.00 73.00 82.00 >>>>>>>>> 2.05213 1.00000 -0.00010 1.00000 >>>>>>>>> 83 5 40.0 39.00 19.00 51.00 >>>>>>>>> 2.04809 1.00000 -0.00010 1.00000 >>>>>>>>> 84 10 80.0 38.00 24.00 69.00 >>>>>>>>> 2.04252 1.00000 -0.00010 1.00000 >>>>>>>>> 85 9 72.0 30.00 32.00 67.00 >>>>>>>>> 2.04237 1.00000 -0.00010 1.00000 >>>>>>>>> 86 7 56.0 54.00 58.00 72.00 >>>>>>>>> 2.03645 1.00000 -0.00010 1.00000 >>>>>>>>> 87 10 80.0 30.00 13.00 22.00 >>>>>>>>> 2.03577 1.00000 -0.00010 1.00000 >>>>>>>>> 88 8 64.0 0.00 25.00 72.00 >>>>>>>>> 2.03193 1.00000 -0.00010 1.00000 >>>>>>>>> 89 5 40.0 7.00 23.00 6.00 >>>>>>>>> 2.02805 1.00000 -0.00010 1.00000 >>>>>>>>> 90 4 32.0 59.00 28.00 21.00 >>>>>>>>> 2.02245 1.00000 -0.00010 1.00000 >>>>>>>>> 91 11 88.0 43.00 18.00 63.00 >>>>>>>>> 2.01764 1.00000 -0.00010 1.00000 >>>>>>>>> 92 5 40.0 14.00 41.00 87.00 >>>>>>>>> 2.01255 1.00000 -0.00010 1.00000 >>>>>>>>> 93 3 24.0 28.00 50.00 55.00 >>>>>>>>> 2.01226 1.00000 -0.00010 1.00000 >>>>>>>>> 94 6 48.0 35.00 0.00 43.00 >>>>>>>>> 1.99869 1.00000 -0.00010 1.00000 >>>>>>>>> 95 1 8.0 59.00 57.00 79.00 >>>>>>>>> 1.99505 1.00000 -0.00010 1.00000 >>>>>>>>> 96 1 8.0 25.00 2.00 51.00 >>>>>>>>> 1.99394 1.00000 -0.00010 1.00000 >>>>>>>>> 97 4 32.0 55.00 4.00 36.00 >>>>>>>>> 1.98505 1.00000 -0.00010 1.00000 >>>>>>>>> 98 2 16.0 66.00 21.00 6.00 >>>>>>>>> 1.97461 1.00000 -0.00010 1.00000 >>>>>>>>> 99 3 24.0 31.00 51.00 90.00 >>>>>>>>> 1.97154 1.00000 -0.00010 1.00000 >>>>>>>>> 100 3 24.0 12.00 11.00 23.00 >>>>>>>>> 1.95664 1.00000 -0.00010 1.00000 >>>>>>>>> 101 5 40.0 38.00 43.00 50.00 >>>>>>>>> 1.95222 1.00000 -0.00010 1.00000 >>>>>>>>> 102 2 16.0 28.00 22.00 7.00 >>>>>>>>> 1.95066 1.00000 -0.00010 1.00000 >>>>>>>>> 103 4 32.0 20.00 17.00 69.00 >>>>>>>>> 1.94669 1.00000 -0.00010 1.00000 >>>>>>>>> 104 5 40.0 1.00 8.00 46.00 >>>>>>>>> 1.94587 1.00000 -0.00010 1.00000 >>>>>>>>> 105 4 32.0 42.00 15.00 49.00 >>>>>>>>> 1.94354 1.00000 -0.00010 1.00000 >>>>>>>>> 106 4 32.0 4.00 41.00 54.00 >>>>>>>>> 1.93906 1.00000 -0.00010 1.00000 >>>>>>>>> 107 3 24.0 15.00 9.00 33.00 >>>>>>>>> 1.93848 1.00000 -0.00010 1.00000 >>>>>>>>> 108 6 48.0 61.00 28.00 72.00 >>>>>>>>> 1.92516 1.00000 -0.00010 1.00000 >>>>>>>>> 109 1 8.0 49.00 26.00 88.00 >>>>>>>>> 1.92457 1.00000 -0.00010 1.00000 >>>>>>>>> 110 3 24.0 65.00 37.00 41.00 >>>>>>>>> 1.92365 1.00000 -0.00010 1.00000 >>>>>>>>> 111 3 24.0 69.00 29.00 25.00 >>>>>>>>> 1.91576 1.00000 -0.00010 1.00000 >>>>>>>>> 112 2 16.0 70.00 15.00 9.00 >>>>>>>>> 1.89931 1.00000 -0.00010 1.00000 >>>>>>>>> 113 2 16.0 65.00 24.00 70.00 >>>>>>>>> 1.89719 1.00000 -0.00010 1.00000 >>>>>>>>> 114 1 8.0 41.00 24.00 36.00 >>>>>>>>> 1.89653 1.00000 -0.00010 1.00000 >>>>>>>>> 115 7 56.0 71.00 32.00 91.00 >>>>>>>>> 1.89529 1.00000 -0.00010 1.00000 >>>>>>>>> 116 6 48.0 24.00 38.00 69.00 >>>>>>>>> 1.88993 1.00000 -0.00010 1.00000 >>>>>>>>> 117 4 32.0 6.00 22.00 34.00 >>>>>>>>> 1.88833 1.00000 -0.00010 1.00000 >>>>>>>>> 118 3 24.0 41.00 45.00 51.00 >>>>>>>>> 1.87881 1.00000 -0.00010 1.00000 >>>>>>>>> 119 2 16.0 18.00 58.00 91.00 >>>>>>>>> 1.87841 1.00000 -0.00010 1.00000 >>>>>>>>> 120 3 24.0 44.00 10.00 17.00 >>>>>>>>> 1.87792 1.00000 -0.00010 1.00000 >>>>>>>>> 121 4 32.0 7.00 38.00 71.00 >>>>>>>>> 1.87444 1.00000 -0.00010 1.00000 >>>>>>>>> 122 2 16.0 39.00 12.00 65.00 >>>>>>>>> 1.87242 1.00000 -0.00010 1.00000 >>>>>>>>> 123 7 56.0 25.00 35.00 38.00 >>>>>>>>> 1.87054 1.00000 -0.00010 1.00000 >>>>>>>>> 124 3 24.0 14.00 28.00 25.00 >>>>>>>>> 1.86776 1.00000 -0.00010 1.00000 >>>>>>>>> 125 4 32.0 64.00 23.00 76.00 >>>>>>>>> 1.86629 1.00000 -0.00010 1.00000 >>>>>>>>> 126 7 56.0 58.00 44.00 43.00 >>>>>>>>> 1.86598 1.00000 -0.00010 1.00000 >>>>>>>>> 127 1 8.0 40.00 44.00 63.00 >>>>>>>>> 1.86487 1.00000 -0.00010 1.00000 >>>>>>>>> 128 1 8.0 19.00 8.00 55.00 >>>>>>>>> 1.84677 1.00000 -0.00010 1.00000 >>>>>>>>> 129 1 8.0 59.00 58.00 80.00 >>>>>>>>> 1.84162 1.00000 -0.00010 1.00000 >>>>>>>>> 130 1 8.0 16.00 40.00 92.00 >>>>>>>>> 1.83828 1.00000 -0.00010 1.00000 >>>>>>>>> 131 2 16.0 21.00 42.00 63.00 >>>>>>>>> 1.83258 1.00000 -0.00010 1.00000 >>>>>>>>> 132 6 48.0 2.00 19.00 69.00 >>>>>>>>> 1.82733 1.00000 -0.00010 1.00000 >>>>>>>>> 133 1 8.0 25.00 45.00 73.00 >>>>>>>>> 1.81604 1.00000 -0.00010 1.00000 >>>>>>>>> 134 1 8.0 6.00 10.00 48.00 >>>>>>>>> 1.81496 1.00000 -0.00010 1.00000 >>>>>>>>> 135 2 16.0 9.00 7.00 43.00 >>>>>>>>> 1.80712 1.00000 -0.00010 1.00000 >>>>>>>>> 136 1 8.0 36.00 2.00 53.00 >>>>>>>>> 1.80667 1.00000 -0.00010 1.00000 >>>>>>>>> 137 1 8.0 19.00 43.00 60.00 >>>>>>>>> 1.80358 1.00000 -0.00010 1.00000 >>>>>>>>> 138 1 8.0 24.00 0.00 25.00 >>>>>>>>> 1.80337 1.00000 -0.00010 1.00000 >>>>>>>>> 139 2 16.0 25.00 5.00 42.00 >>>>>>>>> 1.79990 1.00000 -0.00010 1.00000 >>>>>>>>> 140 4 32.0 69.00 18.00 40.00 >>>>>>>>> 1.79854 1.00000 -0.00010 1.00000 >>>>>>>>> 141 1 8.0 62.00 48.00 85.00 >>>>>>>>> 1.79309 1.00000 -0.00010 1.00000 >>>>>>>>> 142 4 32.0 61.00 43.00 84.00 >>>>>>>>> 1.78916 1.00000 -0.00010 1.00000 >>>>>>>>> 143 1 8.0 13.00 13.00 34.00 >>>>>>>>> 1.78877 1.00000 -0.00010 1.00000 >>>>>>>>> 144 1 8.0 34.00 28.00 78.00 >>>>>>>>> 1.78826 1.00000 -0.00010 1.00000 >>>>>>>>> 145 3 24.0 69.00 32.00 83.00 >>>>>>>>> 1.78152 1.00000 -0.00010 1.00000 >>>>>>>>> 146 1 8.0 14.00 11.00 33.00 >>>>>>>>> 1.78004 1.00000 -0.00010 1.00000 >>>>>>>>> 147 1 8.0 70.00 19.00 25.00 >>>>>>>>> 1.77961 1.00000 -0.00010 1.00000 >>>>>>>>> 148 1 8.0 24.00 1.00 50.00 >>>>>>>>> 1.77625 1.00000 -0.00010 1.00000 >>>>>>>>> 149 1 8.0 3.00 35.00 84.00 >>>>>>>>> 1.77073 1.00000 -0.00010 1.00000 >>>>>>>>> 150 1 8.0 22.00 43.00 64.00 >>>>>>>>> 1.77048 1.00000 -0.00010 1.00000 >>>>>>>>> 151 1 8.0 25.00 63.00 83.00 >>>>>>>>> 1.76957 1.00000 -0.00010 1.00000 >>>>>>>>> 152 1 8.0 52.00 57.00 72.00 >>>>>>>>> 1.76913 1.00000 -0.00010 1.00000 >>>>>>>>> 153 1 8.0 6.00 24.00 31.00 >>>>>>>>> 1.76905 1.00000 -0.00010 1.00000 >>>>>>>>> 154 1 8.0 7.00 37.00 72.00 >>>>>>>>> 1.76885 1.00000 -0.00010 1.00000 >>>>>>>>> 155 2 16.0 75.00 24.00 12.00 >>>>>>>>> 1.76788 1.00000 -0.00010 1.00000 >>>>>>>>> 156 1 8.0 64.00 38.00 42.00 >>>>>>>>> 1.76533 1.00000 -0.00010 1.00000 >>>>>>>>> 157 1 8.0 54.00 32.00 84.00 >>>>>>>>> 1.76446 1.00000 -0.00010 1.00000 >>>>>>>>> 158 1 8.0 23.00 38.00 88.00 >>>>>>>>> 1.76098 1.00000 -0.00010 1.00000 >>>>>>>>> 159 1 8.0 6.00 40.00 33.00 >>>>>>>>> 1.75765 1.00000 -0.00010 1.00000 >>>>>>>>> 160 1 8.0 22.00 25.00 9.00 >>>>>>>>> 1.75009 1.00000 -0.00010 1.00000 >>>>>>>>> 161 2 16.0 67.00 3.00 52.00 >>>>>>>>> 1.74760 1.00000 -0.00010 1.00000 >>>>>>>>> 162 2 16.0 28.00 67.00 70.00 >>>>>>>>> 1.74531 1.00000 -0.00010 1.00000 >>>>>>>>> 163 1 8.0 4.00 33.00 30.00 >>>>>>>>> 1.74303 1.00000 -0.00010 1.00000 >>>>>>>>> 164 1 8.0 69.00 20.00 74.00 >>>>>>>>> 1.74160 1.00000 -0.00010 1.00000 >>>>>>>>> 165 1 8.0 18.00 21.00 55.00 >>>>>>>>> 1.74153 1.00000 -0.00010 1.00000 >>>>>>>>> 166 2 16.0 31.00 25.00 80.00 >>>>>>>>> 1.73939 1.00000 -0.00010 1.00000 >>>>>>>>> 167 2 16.0 22.00 40.00 63.00 >>>>>>>>> 1.73425 1.00000 -0.00010 1.00000 >>>>>>>>> 168 2 16.0 68.00 21.00 74.00 >>>>>>>>> 1.72982 1.00000 -0.00010 1.00000 >>>>>>>>> 169 2 16.0 7.00 18.00 27.00 >>>>>>>>> 1.72964 1.00000 -0.00010 1.00000 >>>>>>>>> 170 1 8.0 11.00 29.00 60.00 >>>>>>>>> 1.72963 1.00000 -0.00010 1.00000 >>>>>>>>> 171 1 8.0 25.00 65.00 86.00 >>>>>>>>> 1.72933 1.00000 -0.00010 1.00000 >>>>>>>>> 172 1 8.0 40.00 10.00 56.00 >>>>>>>>> 1.72897 1.00000 -0.00010 1.00000 >>>>>>>>> 173 2 16.0 40.00 56.00 61.00 >>>>>>>>> 1.72244 1.00000 -0.00010 1.00000 >>>>>>>>> 174 1 8.0 17.00 67.00 74.00 >>>>>>>>> 1.72103 1.00000 -0.00010 1.00000 >>>>>>>>> 175 1 8.0 42.00 67.00 70.00 >>>>>>>>> 1.71913 1.00000 -0.00010 1.00000 >>>>>>>>> 176 1 8.0 25.00 64.00 85.00 >>>>>>>>> 1.71646 1.00000 -0.00010 1.00000 >>>>>>>>> 177 1 8.0 9.00 38.00 73.00 >>>>>>>>> 1.71532 1.00000 -0.00010 1.00000 >>>>>>>>> 178 1 8.0 4.00 34.00 31.00 >>>>>>>>> 1.71458 1.00000 -0.00010 1.00000 >>>>>>>>> 179 1 8.0 3.00 22.00 7.00 >>>>>>>>> 1.71416 1.00000 -0.00010 1.00000 >>>>>>>>> 180 1 8.0 31.00 50.00 89.00 >>>>>>>>> 1.71002 1.00000 -0.00010 1.00000 >>>>>>>>> 181 1 8.0 51.00 7.00 19.00 >>>>>>>>> 1.70870 1.00000 -0.00010 1.00000 >>>>>>>>> 182 1 8.0 43.00 1.00 48.00 >>>>>>>>> 1.70621 1.00000 -0.00010 1.00000 >>>>>>>>> 183 1 8.0 22.00 36.00 41.00 >>>>>>>>> 1.70538 1.00000 -0.00010 1.00000 >>>>>>>>> 184 1 8.0 1.00 22.00 71.00 >>>>>>>>> 1.70431 1.00000 -0.00010 1.00000 >>>>>>>>> 185 1 8.0 65.00 20.00 5.00 >>>>>>>>> 1.70426 1.00000 -0.00010 1.00000 >>>>>>>>> 186 1 8.0 70.00 10.00 43.00 >>>>>>>>> 1.70299 1.00000 -0.00010 1.00000 >>>>>>>>> 187 1 8.0 11.00 17.00 62.00 >>>>>>>>> 1.70210 1.00000 -0.00010 1.00000 >>>>>>>>> 188 1 8.0 1.00 21.00 70.00 >>>>>>>>> 1.70207 1.00000 -0.00010 1.00000 >>>>>>>>> 189 1 8.0 35.00 26.00 63.00 >>>>>>>>> 1.70166 1.00000 -0.00010 1.00000 >>>>>>>>> 190 1 8.0 11.00 37.00 66.00 >>>>>>>>> 1.70059 1.00000 -0.00010 1.00000 >>>>>>>>> 191 1 8.0 22.00 37.00 70.00 >>>>>>>>> 1.70035 1.00000 -0.00010 1.00000 >>>>>>>>> 192 1 8.0 25.00 14.00 22.00 >>>>>>>>> 1.69897 1.00000 -0.00010 1.00000 >>>>>>>>> >>>>>>>>> >>>>>>>>> Date: Tue, 25 Jun 2013 12:22:23 -0400 >>>>>>>>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>>>>>>> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach >>>>>>>>> coordinates >>>>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> Message-ID: <51c9c3bf.7000...@nmr.mgh.harvard.edu >>>>>>>>> <mailto:51c9c3bf.7000...@nmr.mgh.harvard.edu>> >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>>>>>>> >>>>>>>>> can you send the file? >>>>>>>>> >>>>>>>>> On 06/25/2013 10:08 AM, Emily Boeke wrote: >>>>>>>>>> Hi All, >>>>>>>>>> >>>>>>>>>> I'm running Monte Carlo simulations on functional data, and the >>>>>>>>>> coordinate information outputted in the cluster.summary file isn't >>>>>>>>>> making sense. Usually the coordinates for the clusters listed are >>>>>>>>>> Talairach coordinates, but in the .summary files I'm getting, the >>>>>>>>>> coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" >>>>>>>>>> and the numbers are clearly not Talairach coordinates. Above the >>>>>>>>>> table, it says "Reporting Coordinates in Voxel Indices." I also >>>>>>>>>> noted that in the descriptive information above the table, it says >>>>>>>>>> "Registration: None: Tal Coords invalid." >>>>>>>>>> >>>>>>>>>> However, the .nii files I'm seeing look like I would expect them too. >>>>>>>>>> >>>>>>>>>> I'm using the same command line I've run before, so I have no idea >>>>>>>>>> why the .summary file looks different. Does anyone know why this >>>>>>>>>> would be? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Emily >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> gr...@nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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.