Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates
by Douglas N Greve 02 Jul '13

02 Jul '13

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 <greve(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>>>>>> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach >>>>>>>>> coordinates >>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> Message-ID: <51C9C3BF.7000000(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:51C9C3BF.7000000@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(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> 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/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>> -- >>>> 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/ >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> 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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- 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/

1 0

Order of Edits + Intensity Normalization
by Peter Boulos 02 Jul '13

02 Jul '13

Resending, would greatly appreciate some input so I can move forward: I have a fairly basic question regarding the order in which I should perform the edits. After running the full recon on all of my subjects I have now completed the Talairach edits and the skull strip edits on my subjects. At this point I am attempting to seek out help in terms of performing the edits on white/grey matter border from a more experienced user but have a couple of days before I can meet with them. Therefore, can I go ahead and do the pial surface edits before or does the intensity normalization and white/grey boundary edits need to be done first before the pial surface? As in will those edits alter what I do in later steps? Also, I am having a hard time understanding what I am doing with intensity normalization. Am I just ensuring that there are sections of an intensity of 110 in the white matter boundaries of each subject? Am I only looking for white matter that appears to be left out in a disastrous way in this step or should I be very meticulous about this? I am confused because I have areas considered white matter in free surfer that appear to be white matter by visual inspection that have intensities as low as 70 but then areas of the same intensity outside of the boundary. I realize that the program is probably using intensity data along with location data but do not understand how I am supposed to ensure that whether something with an intensity lower than 110 is indeed white matter by visual inspection alone. I apologize for the simplicity of my understanding at this point and thank you for your time. Peter

2 1

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates
by Douglas N Greve 02 Jul '13

02 Jul '13

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 <greve(a)nmr.mgh.harvard.edu >>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach >>>>> coordinates >>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> Message-ID: <51C9C3BF.7000000(a)nmr.mgh.harvard.edu >>>>> <mailto:51C9C3BF.7000000@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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> 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/ >>> >>> _______________________________________________ >>> 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 >> >> > > -- 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 2

Re: [Freesurfer] Some Questions Regarding W Files
by Zhongtian Dai 02 Jul '13

02 Jul '13

Hi Doug, I am using w files to show ECoG activation at localized regions on the cortex. So preferably, I would like to show temporal dynamics too (thus the multi-frame question, and thanks for pointing me to MNE). What will replace w files going forward? i think w file's file format is very concise and clear for what it does. Thanks for the definite answer though. I will spend some time to fork Freeview and add in what I need. Cheers, -- Zhongtian (Falcon) Dai

2 4

Missing ribbon.mgz file
by ye tian 02 Jul '13

02 Jul '13

Dear freesurfers, Recon-all -s subject -autorecon2 returns the following error messages *mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file* mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file. Prior to autorecon2, I did recon-all -s subject -autorecon1, which completed without errors. I found a similar problem in the archive, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/030025.html and I will follow the suggestion given. In the same time, does anybody know what is going wrong? Thank you very much! Sincerely, Ye

2 2

Xhemi files can not be downloaded
by Hamza Alshuft 02 Jul '13

02 Jul '13

Dear Freesurfer experts I can not download files required for surface based inter hemispheric registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome "curl: (78) RETR response: 550" I am currently using Mac version 5.1. Any help please? Thanks, Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

freesurfer registration problem
by Lijia Wang 02 Jul '13

02 Jul '13

Hi experts, When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from BOLD images to the MNI305 template are always only a small part of the original images. I tried to use another T1_152 template instead(higher resolution) of the original MNI305 template, then"recon-all", "preproc-sess", but the results still remain the small part. How can I solve this problem? Thanks! Best Regards! Rebecca

2 1

Re: [Freesurfer] Problem with FS-FAST, mkcontrast
by O'Shea,Andrew 02 Jul '13

02 Jul '13

That was my problem Doug, thanks! I used ' sudo ln -s /Applications/MATLAB_R2011b.app/bin/matlab /usr/local/bin ' and it fixed it. -Andrew Message: 9 Date: Mon, 01 Jul 2013 09:46:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Problem with FS-FAST, mkcontrast To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51D1883F.5050103(a)nmr.mgh.harvard.edu<mailto:51D1883F.5050103@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed doyou have matlab installed and in your path? doug On 07/01/2013 08:55 AM, O'Shea,Andrew wrote: Hello, I am trying to work through the FS-FAST tutorial on my data. I am using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I run ' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 ' I get the following output error: " phhp-jcraggs-mb:Project aoshea$ mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 INFO: Found 1 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test/pain-v-rest.mat nconds 1, wcond 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o test/pain-v-rest.mat -wdelay 1 -no-octave Mon Jul 1 08:51:02 EDT 2013 " It is not creating a .mat file in the analysis directory. Any suggestions would be greatly appreciated. Thanks! -Andrew _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@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/

1 0

REPOST: Volume ROI statistics
by Garikoitz Lerma-Usabiaga 01 Jul '13

01 Jul '13

Hi again, is it possible to use mri_convert with a register.dat to create a .mgh volume in the registered space? any help would be appreciated... thanks! Gari On Mon, Jul 1, 2013 at 8:45 PM, Garikoitz Lerma-Usabiaga < garikoitz(a)gmail.com> wrote: > Hi, > I want to obtain volume statistics from a ROI in fsaverage. > I have register.dat and a .nii file (the ROI), but I don't now how to get > to the .label. > > The last try has been: > mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii > --o $SUBJECTS_DIR/fsaverage/label/ROI.mgh > --reg > $SUBJECTS_DIR/fsaverage/mri/transforms/my_own_register_created_with_bbregister.dat --targ > fsaverage > > (but it is failing, error: > corRead(): can't open file $SUBJECTS_DIR/fsaverage/COR-.info) > > My next steps were: > cor2label (in fsaverage) > mri_label2label (per every subject) > mri_segstats (per every subject) > > > Is there any simpler method to accomplish the same? Or at least that it > works? > many thanks, > Gari >

3 2

Recon-all -autorecon1: Talairach Failure Detection yet "finished without error"
by ye tian 01 Jul '13

01 Jul '13

Dear freesurfers, After running recon-all -s Subject -autorecon1, I checked the status.log file, it seems to have two contradictory statements: #@# *Talairach Failure Detection* Mon Jul 1 13:00:30 CDT 2013 recon-all -s Barba50527_2 finished *without error* at Mon Jul 1 13:23:15 CDT 2013 When I loaded talairach.xfm into brainmask.mgz, talairach.xfm seems to be fine. I had no idea what is going wrong, so I continued to run autorecon2. Would someone please elucidate? Thank you very much! Sincerely, Ye

2 2

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