Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

what may be a corresponding t-value in 2D map after interpolation from voxel to vertex?
by Yune Lee 01 Jul '13

01 Jul '13

Dear Freesurfer users -- I'm trying to display a SPM t map (i.e., normalized in SPM8 standard template) in freesurfer inflated surface for paper figure. So, once projecting the SPM t maps into freesurfer template (e.g., rh.inflated), I'm wondering how I can best find out freesurfer's threshold that matches the original threshold (e.g., t>4 in SPM8) given that the values in every voxel were interpolated to a different value across neighboring vertices during surface reconstruction (e.g., 4 in one voxel is mapped onto 3.92 or 4.1). Is there any rule of thumb to figure out a corresponding value between 3D (voxel) and 2D (vertex)? I'm sure that I'm not the only one dealing with this problem and sharing any of your wisdom will be greatly appreciated. -ysl

1 0

recon-all w/ non-default templates
by Mark Plantz 01 Jul '13

01 Jul '13

Hello all, I currently have volumetric infant templates in .nifti format. Is there any way to run recon-all using these templates instead of the default adult templates? From what I understand, freesurfer uses .tif format for templates. I just can't seem to figure out how to get the infant templates (.nifti format) to work with the FreeSurfer recon-all process. Thank you. - Mark Plantz

1 0

Problem with FS-FAST, mkcontrast
by O'Shea,Andrew 01 Jul '13

01 Jul '13

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

2 1

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates
by Emily Boeke 01 Jul '13

01 Jul '13

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> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51C9C3BF.7000000(a)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

2 3

Re: [Freesurfer] mri_label2vol problem
by LAOUCHEDI MAKHLOUF 01 Jul '13

01 Jul '13

excuse me Doug. i gathered previous correspondences (i wrote your replies are in bold) : june, 28 at 16:41 here is the command and it's terminal : mri_label2vol --annot G_and_S_cingul-Ant.annot --temp /home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 Number of labels: 0 Annot File: G_and_S_cingul-Ant.annot Template Volume: /home/mlaouche/makh_free/ctr2/mri/brain.mgz Outut Volume: /home/mlaouche/G_and_S_cingul-Ant.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: ctr2 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /home/mlaouche/makh_free/ctr2/surf/lh.white nvertices = 138786 Reading thickness /home/mlaouche/makh_free/ctr2/surf/lh.thickness Loading annotations from G_and_S_cingul-Ant.annot reading colortable from annotation file... colortable with 14176 entries read (originally /home_cluster/amesse/software/freesurfer5.1/FreeSurferColorLUT.txt) annotidmax = 1 Allocating Hit Volume (16777216) voxels nlabels = 1 PVF (null) Thesholding hit volume. done june, 28 at 16:41 The terminal output, ie, what gets printed to the screen after your run the program. june, 28 at 16:39 excuse me but i don't understand what you mean by "terminal of mri_label2volume" Thank you for help june, 28 at 16:33 please post responses to the list doug btw, there is no terminal output below june, 28 at 16:29 i used tksurfer to display the volume and i imported the annotation file created, it looks ok. about the full terminal ouput of mri_label2vol : /home/mlaouche/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 Thanks (in fact i used to assemble individual labels to make some annotation files for some parts of the brain, which i used to transform to nifti using mri_label2vol without problem) june, 28 at 16:49 Doug How does the annot look on the surface (ie, intksurfer)? What is the full terminal output of mri_label2vol? june, 28 at 16:19 Hi i run mri_label2annot to get individual annot files for all labels, then i run mri_label2vol to get nifti volumes of my labels using the following command : mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 but the result is a volume with zero values (i changed --fillthresh .5 to --fillthresh 0 and i got the same probleme) Thanks ________________________________ De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> À : LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> Envoyé le : Vendredi 28 juin 2013 18h41 Objet : Re: [Freesurfer] mri_label2vol problem Hi Laouchedi, I have asked you two times now to include all previous correspondences in each email. This is the 3rd time. If you are going to make it hard for us to answer your question, then the result will be that they won't be answered. thanks doug On 06/28/2013 12:12 PM, LAOUCHEDI MAKHLOUF wrote: > here is the command and it's terminal : > > mri_label2vol --annot G_and_S_cingul-Ant.annot --temp > /home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh > --identity --fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz > --proj frac 0 1 .1 > > Number of labels: 0 > Annot File: G_and_S_cingul-Ant.annot > Template Volume: /home/mlaouche/makh_free/ctr2/mri/brain.mgz > Outut Volume: /home/mlaouche/G_and_S_cingul-Ant.nii.gz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: frac > ProjTypeId: 2 > ProjStart: 0 > ProjStop: 1 > ProjDelta: 0.1 > Subject: ctr2 > Hemi: lh > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0 > Using Identity Matrix > RegMat: -------- > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > 0.000 0.000 -1.000 128.000; > 0.000 1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > INFO: loading surface /home/mlaouche/makh_free/ctr2/surf/lh.white > nvertices = 138786 > Reading thickness /home/mlaouche/makh_free/ctr2/surf/lh.thickness > Loading annotations from G_and_S_cingul-Ant.annot > reading colortable from annotation file... > colortable with 14176 entries read (originally > /home_cluster/amesse/software/freesurfer5.1/FreeSurferColorLUT.txt) > annotidmax = 1 > Allocating Hit Volume (16777216) voxels > nlabels = 1 > > PVF (null) > Thesholding hit volume. > done > > > ------------------------------------------------------------------------ > *De :* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *À :* freesurfer(a)nmr.mgh.harvard.edu > *Envoyé le :* Vendredi 28 juin 2013 16h49 > *Objet :* Re: [Freesurfer] mri_label2vol problem > > How does the annot look on the surface (ie, intksurfer)? What is the > full terminal output of mri_label2vol? > > On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote: > > Hi > > i run mri_label2annot to get individual annot files for all > > labels, then i run mri_label2vol to get nifti volumes of my labels > > using the following command : > > mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp > > SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity > > --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 > > > > but the result is a volume with zero values (i changed --fillthresh .5 > > to --fillthresh 0 and i got the same probleme) > > > > Thanks > > > > > > _______________________________________________ > > 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/ > > _______________________________________________ > 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 > <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. > > > -- 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

Rejoindre mon réseau sur LinkedIn
by Justin Eisenberg via LinkedIn 30 Jun '13

30 Jun '13

LinkedIn ------------ Justin Eisenberg souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Justin Eisenberg http://www.linkedin.com/e/-qq80um-hil2pf3v-5a/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Justin Eisenberg http://www.linkedin.com/e/-qq80um-hil2pf3v-5a/rso/239440173/pDSN/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hil2pf3v-5a/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

1 0

Re: [Freesurfer] tksurfer display problem
by Xiangzhen Kong 29 Jun '13

29 Jun '13

Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" <bnucon(a)gmail.com> wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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.

3 10

Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
by Koolschijn, Cédric 28 Jun '13

28 Jun '13

Hi Martin, Unfortunately it is not a single subject, it happens to many. If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software. FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs. I'll get back to you when results of FS 5.3 are available. Cheers, Cédric On 6/28/13 2:43 AM, "Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> wrote: Hi Cedric, Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)? It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long). Best, Martin On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote: Hi Martin, Thanks for your fast response. It makes sense that in the longi-stream results should be more reliable. However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion. Any thoughts on this? Cheers, Cédric From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn <P.C.M.P.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl>> Cc: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing Hi Cedric, this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable. Cheers, Martin On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers, I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there. Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently. Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal? Many thanks! Cheers, Cédric ------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl> W http://www.dutcharc.nl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu 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. -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu

3 2

re gcareg ?
by Dov Sadan 28 Jun '13

28 Jun '13

Hi, Thank you all for the wonderful project! >From time to time while reading some of the wiki pages it has the feeling of reading ancient Chinese. https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg I'd be happy if anyone help me understand what GCA ? and ismri/no. are ? Thanks in advance, Dov

4 6

Order of Edits + Intensity Normalization
by Peter Boulos 28 Jun '13

28 Jun '13

Hello, 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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer