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T2raw.dat.log

T2raw.dat.log 41 KB
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  1. Logfile for bbregister
    2. 

  2. Thu Aug  8 21:37:12 CEST 2013
    3. 

  3. 

  4. setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
    5. 

  5. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    6. 

  6. /opt/freesurfer/5.3.0/bin/bbregister --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta --init-fsl --T2
    7. 

  7. 

  8. $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
    9. 

  9. Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
    10. 

  10. FREESURFER_HOME /opt/freesurfer/5.3.0
    11. 

  11. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
    12. 

  12. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii 
    13. 

  13. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    14. 

  14. reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz...
    15. 

  15. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    16. 

  16. i_ras = (-0.996814, 0.0369416, 0.0706971)
    17. 

  17. j_ras = (0.0317143, 0.996777, -0.0736842)
    18. 

  18. k_ras = (0.0731912, 0.0712073, 0.994773)
    19. 

  19. writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii...
    20. 

  20. fslregister --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister --dof 6 --fsvol brainmask.mgz
    21. 

  21. 

  22. Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fslregister.log
    23. 

  23. 

  24. Thu Aug  8 21:37:17 CEST 2013
    25. 

  25. --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister --dof 6 --fsvol brainmask.mgz
    26. 

  26. $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
    27. 

  27. snake5
    28. 

  28. Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
    29. 

  29. nIters 1
    30. 

  30. --------------------------------------
    31. 

  31. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    32. 

  32. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii
    33. 

  33. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii 
    34. 

  34. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    35. 

  35. reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/brainmask.mgz...
    36. 

  36. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    37. 

  37. i_ras = (-1, -5.58794e-09, -7.45058e-09)
    38. 

  38. j_ras = (7.45058e-09, 1.49012e-08, -1)
    39. 

  39. k_ras = (-1.86265e-09, 1, 7.45058e-09)
    40. 

  40. writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii...
    41. 

  41. --------------------------------------
    42. 

  42. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    43. 

  43. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --frame 0
    44. 

  44. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --frame 0 
    45. 

  45. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    46. 

  46. reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii...
    47. 

  47. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    48. 

  48. i_ras = (-0.996814, 0.0369416, 0.0706971)
    49. 

  49. j_ras = (0.0317143, 0.996777, -0.0736842)
    50. 

  50. k_ras = (0.0731912, 0.0712073, 0.994773)
    51. 

  51. keeping frame 0
    52. 

  52. writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii...
    53. 

  53. Mov determinant is -0.311089
    54. 

  54. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    55. 

  55. tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/reg0.7795.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat0 --s sub004 --noedit
    56. 

  56. tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
    57. 

  57. INFO: no target volume specified, assuming FreeSurfer orig volume.
    58. 

  58. target  volume orig
    59. 

  59. movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii
    60. 

  60. reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/reg0.7795.dat
    61. 

  61. LoadVol        0
    62. 

  62. ZeroCRAS       0
    63. 

  63. $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
    64. 

  64. Diagnostic Level -1
    65. 

  65. INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
    66. 

  66. Ttarg: --------------------
    67. 

  67. -1.000   0.000   0.000   128.000;
    68. 

  68.  0.000   0.000   1.000  -128.000;
    69. 

  69.  0.000  -1.000   0.000   128.000;
    70. 

  70.  0.000   0.000   0.000   1.000;
    71. 

  71. INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii
    72. 

  72. Tmov: --------------------
    73. 

  73. -0.700   0.000   0.000   95.893;
    74. 

  74.  0.000   0.000   0.667  -128.000;
    75. 

  75.  0.000  -0.667   0.000   128.000;
    76. 

  76.  0.000   0.000   0.000   1.000;
    77. 

  77. mkheaderreg = 1, float2int = 0
    78. 

  78. Computing reg from header (and possibly input matrix)
    79. 

  79. ---- Input registration matrix (computed) --------
    80. 

  80.  0.997  -0.037  -0.071   0.000;
    81. 

  81.  0.073   0.071   0.995  -0.000;
    82. 

  82. -0.032  -0.997   0.074  -0.000;
    83. 

  83.  0.000   0.000   0.000   1.000;
    84. 

  84. ---------------------------------------
    85. 

  85. ---- Input registration matrix --------
    86. 

  86.  0.997  -0.037  -0.071   0.000;
    87. 

  87.  0.073   0.071   0.995  -0.000;
    88. 

  88. -0.032  -0.997   0.074  -0.000;
    89. 

  89.  0.000   0.000   0.000   1.000;
    90. 

  90. Determinant 1
    91. 

  91. subject = sub004
    92. 

  92. RegMat ---------------------------
    93. 

  93.  0.997  -0.037  -0.071   0.000;
    94. 

  94.  0.073   0.071   0.995  -0.000;
    95. 

  95. -0.032  -0.997   0.074  -0.000;
    96. 

  96.  0.000   0.000   0.000   1.000;
    97. 

  97. FSLOUTPUTTYPE NIFTI 
    98. 

  98. tkreg2FSL: mov det = -0.311089, ref det = -1
    99. 

  99. Thu Aug  8 21:37:25 CEST 2013
    100. 

  100. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    101. 

  101. flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat0
    102. 

  102. Thu Aug  8 21:41:57 CEST 2013
    103. 

  103. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    104. 

  104. flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
    105. 

  105. tkregister2_cmdl --s sub004 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat.fsl.mat --noedit
    106. 

  106. tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
    107. 

  107. ---- FSL registration matrix --------
    108. 

  108.  0.997  -0.029  -0.076   45.787;
    109. 

  109. -0.074   0.070  -0.995   254.922;
    110. 

  110.  0.034   0.997   0.067  -11.324;
    111. 

  111.  0.000   0.000   0.000   1.000;
    112. 

  112. ---------------------------------------
    113. 

  113. INFO: no target volume specified, assuming FreeSurfer orig volume.
    114. 

  114. target  volume orig
    115. 

  115. movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
    116. 

  116. reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat
    117. 

  117. LoadVol        0
    118. 

  118. ZeroCRAS       0
    119. 

  119. $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
    120. 

  120. Diagnostic Level -1
    121. 

  121. INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
    122. 

  122. Ttarg: --------------------
    123. 

  123. -1.000   0.000   0.000   128.000;
    124. 

  124.  0.000   0.000   1.000  -128.000;
    125. 

  125.  0.000  -1.000   0.000   128.000;
    126. 

  126.  0.000   0.000   0.000   1.000;
    127. 

  127. INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
    128. 

  128. Tmov: --------------------
    129. 

  129. -0.700   0.000   0.000   95.893;
    130. 

  130.  0.000   0.000   0.667  -128.000;
    131. 

  131.  0.000  -0.667   0.000   128.000;
    132. 

  132.  0.000   0.000   0.000   1.000;
    133. 

  133. mkheaderreg = 0, float2int = 0
    134. 

  134. FSLOUTPUTTYPE NIFTI 
    135. 

  135. fsl2TkReg: mov det = -0.311089, ref det = -1
    136. 

  136. ---- Input registration matrix (computed) --------
    137. 

  137.  0.997  -0.034  -0.074  -0.150;
    138. 

  138.  0.076   0.067   0.995   1.396;
    139. 

  139. -0.029  -0.997   0.070   0.282;
    140. 

  140.  0.000   0.000   0.000   1.000;
    141. 

  141. ---------------------------------------
    142. 

  142. ---- Input registration matrix --------
    143. 

  143.  0.997  -0.034  -0.074  -0.150;
    144. 

  144.  0.076   0.067   0.995   1.396;
    145. 

  145. -0.029  -0.997   0.070   0.282;
    146. 

  146.  0.000   0.000   0.000   1.000;
    147. 

  147. Determinant 1
    148. 

  148. subject = sub004
    149. 

  149. RegMat ---------------------------
    150. 

  150.  0.997  -0.034  -0.074  -0.150;
    151. 

  151.  0.076   0.067   0.995   1.396;
    152. 

  152. -0.029  -0.997   0.070   0.282;
    153. 

  153.  0.000   0.000   0.000   1.000;
    154. 

  154.  
    155. 

  155. Started at Thu Aug 8 21:37:17 CEST 2013 
    156. 

  156. Ended   at Thu Aug  8 21:48:03 CEST 2013
    157. 

  157.  
    158. 

  158. fslregister Done
    159. 

  159.  
    160. 

  160. To check results, run:
    161. 

  161. tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --surf orig
    162. 

  162.  
    163. 

  163. mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
    164. 

  164. $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
    165. 

  165. setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
    166. 

  166. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    167. 

  167. mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
    168. 

  168. sysname  Linux
    169. 

  169. hostname snake5
    170. 

  170. machine  x86_64
    171. 

  171. user     fkaule
    172. 

  172. movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
    173. 

  173. regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.init.dat
    174. 

  174. subject sub004
    175. 

  175. dof 6
    176. 

  176. outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat
    177. 

  177. UseMask 0
    178. 

  178. UseLH 1
    179. 

  179. UseRH 1
    180. 

  180. nsubsamp 100
    181. 

  181. PenaltySign  -1
    182. 

  182. PenaltySlope 0.500000
    183. 

  183. PenaltyCenter 0.000000
    184. 

  184. surfname white
    185. 

  185. GMProjFrac 0.500000
    186. 

  186. WMProjAbs 2.000000
    187. 

  187. lhcostfile (null)
    188. 

  188. rhcostfile (null)
    189. 

  189. interp  trilinear (1)
    190. 

  190. frame  0
    191. 

  191. TolPowell 0.000100
    192. 

  192. nMaxItersPowell 36
    193. 

  193. n1dmin  3
    194. 

  194. Profile   0
    195. 

  195. Gdiag_no  -1
    196. 

  196. AddNoise  0 (0)
    197. 

  197. SynthSeed 1376763169
    198. 

  198. TransRandMax 0.000000
    199. 

  199. RotRandMax 0.000000
    200. 

  200. Translations 0.000000 0.000000 0.000000
    201. 

  201. Rotations   0.000000 0.000000 0.000000
    202. 

  202. Input reg
    203. 

  203.  0.997  -0.034  -0.074  -0.150;
    204. 

  204.  0.076   0.067   0.995   1.396;
    205. 

  205. -0.029  -0.997   0.070   0.282;
    206. 

  206.  0.000   0.000   0.000   1.000;
    207. 

  207. 

  208. Loading mov
    209. 

  209. Projecting LH Surfs
    210. 

  210. Loading lh.white surf
    211. 

  211. Loading lh.thickness for GM
    212. 

  212. GM Proj: 1 0.500000 2.000000
    213. 

  213. WM Proj: 0 0.500000 2.000000
    214. 

  214. Projecting RH Surfs
    215. 

  215. Loading rh.white surf
    216. 

  216. Loading rh.thickness
    217. 

  217. Projecting RH Surfs
    218. 

  218. Computing relative cost
    219. 

  219.  0  -25.0 -25.0 -25.0   0.990335
    220. 

  220.  1  -25.0 -25.0  25.0   1.046258
    221. 

  221.  2  -25.0  25.0 -25.0   1.034979
    222. 

  222.  3  -25.0  25.0  25.0   1.009670
    223. 

  223.  4   25.0 -25.0 -25.0   1.002974
    224. 

  224.  5   25.0 -25.0  25.0   0.984347
    225. 

  225.  6   25.0  25.0 -25.0   1.026177
    226. 

  226.  7   25.0  25.0  25.0   0.983004
    227. 

  227. REL:  8  0.395479    8.077746  1.009718 rel = 0.391672 
    228. 

  228. Initial costs ----------------
    229. 

  229. Number of surface hits 2556
    230. 

  230. WM  Intensity    63.9983 +/-  10.9597
    231. 

  231. Ctx Intensity    77.7737 +/-  15.9144
    232. 

  232. Pct Contrast     18.6680 +/-  22.7255
    233. 

  233. Cost   0.3955
    234. 

  234. RelCost   0.3917
    235. 

  235. 

  236. ------------------------------------
    237. 

  237. Brute force preopt -4 4 4, n = 729
    238. 

  238.      0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9607   0.9607  0.0
    239. 

  239.     15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9091   0.9091  0.0
    240. 

  240.     19  -4.0000  -4.0000  -4.0000   4.0000  -4.0000   0.0000      0.8647   0.8647  0.0
    241. 

  241.     21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8209   0.8209  0.0
    242. 

  242.     39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.7859   0.7859  0.0
    243. 

  243.    102  -4.0000   0.0000  -4.0000   4.0000   0.0000  -4.0000      0.7537   0.7537  0.0
    244. 

  244.    120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6957   0.6957  0.0
    245. 

  245.    283   0.0000  -4.0000   0.0000   0.0000   0.0000   0.0000      0.6039   0.6039  0.0
    246. 

  246.    364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3955   0.3955  0.0
    247. 

  247. Brute Force --------------------------
    248. 

  248. Min cost was 0.395479
    249. 

  249. Number of iterations   729
    250. 

  250. Search time 2.737000 sec
    251. 

  251. Parameters at best (transmm, rotdeg)
    252. 

  252.   0.000   0.000   0.000  0.000  0.000  0.000 
    253. 

  253. --------------------------------------------
    254. 

  254. 

  255. Starting Powell Minimization
    256. 

  256. Init Powel Params dof = 6
    257. 

  257. 0 0
    258. 

  258. 1 0
    259. 

  259. 2 0
    260. 

  260. 3 0
    261. 

  261. 4 0
    262. 

  262. 5 0
    263. 

  263.   10  0.007  0.000  0.000  0.000  0.000  0.000   0.3954699444
    264. 

  264.   12  0.005  0.000  0.000  0.000  0.000  0.000   0.3954657001
    265. 

  265.   13  0.004  0.000  0.000  0.000  0.000  0.000   0.3954656519
    266. 

  266.   17  0.004 -1.618  0.000  0.000  0.000  0.000   0.1426153987
    267. 

  267.   24  0.004 -1.616  0.000  0.000  0.000  0.000   0.1426134406
    268. 

  268.   25  0.004 -1.613  0.000  0.000  0.000  0.000   0.1426091991
    269. 

  269.   34  0.004 -1.613  0.382  0.000  0.000  0.000   0.1302286759
    270. 

  270.   36  0.004 -1.613  0.268  0.000  0.000  0.000   0.1286964379
    271. 

  271.   38  0.004 -1.613  0.303  0.000  0.000  0.000   0.1284859533
    272. 

  272.   39  0.004 -1.613  0.297  0.000  0.000  0.000   0.1284730009
    273. 

  273.   40  0.004 -1.613  0.296  0.000  0.000  0.000   0.1284716918
    274. 

  274.   47  0.004 -1.613  0.296  0.382  0.000  0.000   0.0992088363
    275. 

  275.   48  0.004 -1.613  0.296  0.450  0.000  0.000   0.0980428336
    276. 

  276.   49  0.004 -1.613  0.296  0.481  0.000  0.000   0.0976778180
    277. 

  277.   52  0.004 -1.613  0.296  0.521  0.000  0.000   0.0976072447
    278. 

  278.   53  0.004 -1.613  0.296  0.507  0.000  0.000   0.0974022707
    279. 

  279.   55  0.004 -1.613  0.296  0.505  0.000  0.000   0.0973990432
    280. 

  280.   65  0.004 -1.613  0.296  0.505 -0.007  0.000   0.0973140773
    281. 

  281.   66  0.004 -1.613  0.296  0.505 -0.023  0.000   0.0972947579
    282. 

  282.   68  0.004 -1.613  0.296  0.505 -0.016  0.000   0.0972744908
    283. 

  283.   77  0.004 -1.613  0.296  0.505 -0.016  0.031   0.0969850361
    284. 

  284.   79  0.004 -1.613  0.296  0.505 -0.016  0.034   0.0969796928
    285. 

  285.   91  0.015 -1.613  0.296  0.505 -0.016  0.034   0.0969708019
    286. 

  286.   92  0.011 -1.613  0.296  0.505 -0.016  0.034   0.0969688010
    287. 

  287.   93  0.010 -1.613  0.296  0.505 -0.016  0.034   0.0969678084
    288. 

  288.   95  0.009 -1.613  0.296  0.505 -0.016  0.034   0.0969673702
    289. 

  289.  102  0.009 -1.583  0.296  0.505 -0.016  0.034   0.0957225221
    290. 

  290.  103  0.009 -1.512  0.296  0.505 -0.016  0.034   0.0956431997
    291. 

  291.  105  0.009 -1.546  0.296  0.505 -0.016  0.034   0.0951402153
    292. 

  292.  106  0.009 -1.547  0.296  0.505 -0.016  0.034   0.0951385373
    293. 

  293.  107  0.009 -1.549  0.296  0.505 -0.016  0.034   0.0951360701
    294. 

  294.  110  0.009 -1.550  0.296  0.505 -0.016  0.034   0.0951357010
    295. 

  295.  118  0.009 -1.550  0.012  0.505 -0.016  0.034   0.0873739917
    296. 

  296.  119  0.009 -1.550  0.018  0.505 -0.016  0.034   0.0873375201
    297. 

  297.  120  0.009 -1.550  0.040  0.505 -0.016  0.034   0.0872135720
    298. 

  298.  121  0.009 -1.550  0.138  0.505 -0.016  0.034   0.0862267258
    299. 

  299.  125  0.009 -1.550  0.125  0.505 -0.016  0.034   0.0861260298
    300. 

  300.  126  0.009 -1.550  0.124  0.505 -0.016  0.034   0.0861259001
    301. 

  301.  135  0.009 -1.550  0.124  0.566 -0.016  0.034   0.0858010437
    302. 

  302.  137  0.009 -1.550  0.124  0.541 -0.016  0.034   0.0855510203
    303. 

  303.  139  0.009 -1.550  0.124  0.532 -0.016  0.034   0.0855427346
    304. 

  304.  141  0.009 -1.550  0.124  0.535 -0.016  0.034   0.0855387127
    305. 

  305.  151  0.009 -1.550  0.124  0.535 -0.019  0.034   0.0855114469
    306. 

  306.  152  0.009 -1.550  0.124  0.535 -0.034  0.034   0.0854628992
    307. 

  307.  154  0.009 -1.550  0.124  0.535 -0.030  0.034   0.0854598576
    308. 

  308.  156  0.009 -1.550  0.124  0.535 -0.029  0.034   0.0854598167
    309. 

  309.  165  0.009 -1.550  0.124  0.535 -0.029  0.049   0.0851642324
    310. 

  310.  166  0.009 -1.550  0.124  0.535 -0.029  0.102   0.0849879596
    311. 

  311.  168  0.009 -1.550  0.124  0.535 -0.029  0.082   0.0848723293
    312. 

  312.  169  0.009 -1.550  0.124  0.535 -0.029  0.081   0.0848697572
    313. 

  313.  172  0.009 -1.550  0.124  0.535 -0.029  0.080   0.0848696467
    314. 

  314.  173  0.015 -1.486 -0.049  0.565 -0.042  0.126   0.0833334988
    315. 

  315.  180  0.014 -1.496 -0.020  0.560 -0.040  0.118   0.0832923721
    316. 

  316.  181  0.014 -1.495 -0.024  0.561 -0.040  0.120   0.0832759040
    317. 

  317.  182  0.015 -1.492 -0.031  0.562 -0.040  0.121   0.0832675161
    318. 

  318.  183  0.015 -1.493 -0.030  0.562 -0.040  0.121   0.0832667772
    319. 

  319.  184  0.015 -1.493 -0.029  0.562 -0.040  0.121   0.0832663080
    320. 

  320.  185  0.015 -1.493 -0.029  0.562 -0.040  0.121   0.0832662665
    321. 

  321.  187  0.015 -1.493 -0.029  0.562 -0.040  0.121   0.0832661555
    322. 

  322.  189  0.015 -1.493 -0.029  0.562 -0.040  0.121   0.0832661057
    323. 

  323.  197  0.196 -1.493 -0.029  0.562 -0.040  0.121   0.0829808860
    324. 

  324.  198  0.152 -1.493 -0.029  0.562 -0.040  0.121   0.0820850604
    325. 

  325.  199  0.110 -1.493 -0.029  0.562 -0.040  0.121   0.0817788489
    326. 

  326.  200  0.108 -1.493 -0.029  0.562 -0.040  0.121   0.0817786502
    327. 

  327.  202  0.109 -1.493 -0.029  0.562 -0.040  0.121   0.0817783720
    328. 

  328.  210  0.109 -1.487 -0.029  0.562 -0.040  0.121   0.0817533131
    329. 

  329.  213  0.109 -1.486 -0.029  0.562 -0.040  0.121   0.0817527766
    330. 

  330.  220  0.109 -1.486 -0.029  0.562 -0.040  0.113   0.0817381302
    331. 

  331.  222  0.109 -1.486 -0.029  0.562 -0.040  0.114   0.0817377352
    332. 

  332.  230  0.109 -1.486 -0.029  0.623 -0.040  0.114   0.0788986594
    333. 

  333.  231  0.109 -1.486 -0.029  0.675 -0.040  0.114   0.0788313512
    334. 

  334.  232  0.109 -1.486 -0.029  0.650 -0.040  0.114   0.0786353742
    335. 

  335.  234  0.109 -1.486 -0.029  0.649 -0.040  0.114   0.0786323986
    336. 

  336.  236  0.109 -1.486 -0.029  0.645 -0.040  0.114   0.0786236453
    337. 

  337.  248  0.109 -1.486 -0.029  0.645 -0.045  0.114   0.0786126261
    338. 

  338.  251  0.109 -1.486 -0.029  0.645 -0.046  0.114   0.0786115614
    339. 

  339.  258  0.111 -1.462 -0.095  0.657 -0.050  0.131   0.0776070620
    340. 

  340.  259  0.111 -1.462 -0.093  0.656 -0.050  0.131   0.0775988412
    341. 

  341.  260  0.110 -1.465 -0.085  0.655 -0.050  0.129   0.0775621260
    342. 

  342.  263  0.110 -1.466 -0.082  0.654 -0.050  0.128   0.0775605046
    343. 

  343.  266  0.110 -1.466 -0.083  0.654 -0.050  0.128   0.0775604261
    344. 

  344.  268  0.211 -1.382 -0.289  0.774 -0.070  0.177   0.0766942562
    345. 

  345.  274  0.173 -1.414 -0.210  0.728 -0.062  0.158   0.0762590916
    346. 

  346.  275  0.187 -1.403 -0.239  0.745 -0.065  0.165   0.0760664021
    347. 

  347.  277  0.196 -1.395 -0.258  0.756 -0.067  0.169   0.0759852322
    348. 

  348.  279  0.194 -1.397 -0.253  0.753 -0.066  0.168   0.0759797410
    349. 

  349.  281  0.195 -1.396 -0.255  0.754 -0.067  0.169   0.0759778584
    350. 

  350.  293  0.168 -1.396 -0.255  0.754 -0.067  0.169   0.0758012494
    351. 

  351.  294  0.167 -1.396 -0.255  0.754 -0.067  0.169   0.0757999063
    352. 

  352.  295  0.164 -1.396 -0.255  0.754 -0.067  0.169   0.0757958398
    353. 

  353.  298  0.163 -1.396 -0.255  0.754 -0.067  0.169   0.0757955273
    354. 

  354.  308  0.163 -1.373 -0.255  0.754 -0.067  0.169   0.0756043267
    355. 

  355.  311  0.163 -1.374 -0.255  0.754 -0.067  0.169   0.0756019237
    356. 

  356.  321  0.163 -1.374 -0.255  0.754 -0.067  0.164   0.0756000897
    357. 

  357.  323  0.163 -1.374 -0.255  0.754 -0.067  0.166   0.0755996286
    358. 

  358.  329  0.159 -1.414 -0.149  0.735 -0.059  0.137   0.0746940753
    359. 

  359.  333  0.159 -1.411 -0.155  0.737 -0.059  0.139   0.0746885499
    360. 

  360.  334  0.159 -1.412 -0.153  0.736 -0.059  0.139   0.0746843485
    361. 

  361.  335  0.159 -1.412 -0.153  0.736 -0.059  0.138   0.0746830986
    362. 

  362.  337  0.159 -1.412 -0.152  0.736 -0.059  0.138   0.0746830979
    363. 

  363.  339  0.159 -1.412 -0.152  0.736 -0.059  0.138   0.0746829520
    364. 

  364.  347  0.159 -1.412 -0.152  0.736 -0.060  0.138   0.0746743997
    365. 

  365.  348  0.159 -1.412 -0.152  0.736 -0.072  0.138   0.0746272444
    366. 

  366.  350  0.159 -1.412 -0.152  0.736 -0.071  0.138   0.0746269633
    367. 

  367.  363  0.160 -1.412 -0.154  0.737 -0.071  0.139   0.0746260905
    368. 

  368.  376  0.139 -1.412 -0.154  0.737 -0.071  0.139   0.0744794309
    369. 

  369.  387  0.139 -1.398 -0.154  0.737 -0.071  0.139   0.0743690639
    370. 

  370.  397  0.139 -1.398 -0.154  0.737 -0.071  0.208   0.0743571635
    371. 

  371.  399  0.139 -1.398 -0.154  0.737 -0.071  0.173   0.0739818935
    372. 

  372.  402  0.139 -1.398 -0.154  0.737 -0.071  0.167   0.0739658896
    373. 

  373.  411  0.139 -1.402 -0.141  0.735 -0.070  0.164   0.0737362309
    374. 

  374.  413  0.138 -1.408 -0.126  0.732 -0.069  0.159   0.0736378142
    375. 

  375.  414  0.138 -1.408 -0.126  0.732 -0.069  0.159   0.0736375626
    376. 

  376.  427  0.138 -1.408 -0.126  0.732 -0.071  0.159   0.0736364869
    377. 

  377.  430  0.138 -1.408 -0.126  0.732 -0.070  0.159   0.0736363646
    378. 

  378.  436  0.177 -1.376 -0.205  0.778 -0.078  0.178   0.0735789822
    379. 

  379.  437  0.159 -1.391 -0.168  0.756 -0.075  0.169   0.0734949224
    380. 

  380.  439  0.151 -1.398 -0.152  0.747 -0.073  0.165   0.0734198939
    381. 

  381.  441  0.151 -1.397 -0.152  0.747 -0.073  0.165   0.0734197493
    382. 

  382.  445  0.142 -1.383 -0.150  0.757 -0.075  0.192   0.0733829947
    383. 

  383.  477  0.153 -1.397 -0.152  0.747 -0.073  0.185   0.0733214881
    384. 

  384.  478  0.153 -1.397 -0.152  0.747 -0.073  0.183   0.0733108810
    385. 

  385.  479  0.153 -1.397 -0.152  0.747 -0.073  0.180   0.0733066595
    386. 

  386.  488  0.152 -1.400 -0.145  0.746 -0.073  0.178   0.0732080094
    387. 

  387.  490  0.152 -1.405 -0.131  0.743 -0.072  0.175   0.0731436851
    388. 

  388.  506  0.152 -1.405 -0.131  0.743 -0.073  0.175   0.0731431375
    389. 

  389.  507  0.152 -1.405 -0.131  0.743 -0.074  0.175   0.0731430000
    390. 

  390.  516  0.167 -1.393 -0.161  0.761 -0.077  0.182   0.0730938107
    391. 

  391.  517  0.163 -1.396 -0.154  0.757 -0.076  0.180   0.0730515959
    392. 

  392.  518  0.161 -1.398 -0.149  0.754 -0.075  0.179   0.0730406343
    393. 

  393.  519  0.160 -1.398 -0.148  0.753 -0.075  0.179   0.0730405229
    394. 

  394.  525  0.169 -1.399 -0.144  0.759 -0.077  0.192   0.0728348192
    395. 

  395.  530  0.175 -1.399 -0.142  0.763 -0.079  0.200   0.0727927115
    396. 

  396.  532  0.176 -1.400 -0.142  0.764 -0.079  0.202   0.0727911080
    397. 

  397.  535  0.176 -1.400 -0.142  0.764 -0.079  0.201   0.0727911058
    398. 

  398.  536  0.176 -1.400 -0.142  0.764 -0.079  0.202   0.0727909245
    399. 

  399.  537  0.176 -1.400 -0.142  0.764 -0.079  0.202   0.0727909004
    400. 

  400.  559  0.176 -1.387 -0.142  0.764 -0.079  0.202   0.0727378480
    401. 

  401.  560  0.176 -1.389 -0.142  0.764 -0.079  0.202   0.0727336464
    402. 

  402.  561  0.176 -1.390 -0.142  0.764 -0.079  0.202   0.0727304348
    403. 

  403.  563  0.176 -1.391 -0.142  0.764 -0.079  0.202   0.0727302022
    404. 

  404.  584  0.173 -1.394 -0.135  0.760 -0.078  0.200   0.0727220625
    405. 

  405.  586  0.173 -1.394 -0.136  0.761 -0.078  0.200   0.0727217494
    406. 

  406.  606  0.177 -1.394 -0.134  0.763 -0.079  0.205   0.0727162184
    407. 

  407.  607  0.176 -1.394 -0.135  0.762 -0.079  0.204   0.0727155011
    408. 

  408.  608  0.176 -1.394 -0.135  0.762 -0.079  0.204   0.0727154412
    409. 

  409.  611  0.176 -1.394 -0.135  0.762 -0.079  0.204   0.0727154173
    410. 

  410.  612  0.176 -1.394 -0.135  0.762 -0.079  0.204   0.0727153439
    411. 

  411.  625  0.177 -1.394 -0.135  0.762 -0.079  0.204   0.0727145586
    412. 

  412.  636  0.177 -1.392 -0.135  0.762 -0.079  0.204   0.0727101900
    413. 

  413.  648  0.177 -1.392 -0.135  0.762 -0.079  0.203   0.0727091493
    414. 

  414.  657  0.176 -1.392 -0.133  0.762 -0.079  0.202   0.0727083412
    415. 

  415.  670  0.176 -1.392 -0.133  0.762 -0.081  0.202   0.0727072398
    416. 

  416.  678  0.178 -1.393 -0.133  0.762 -0.081  0.204   0.0727063435
    417. 

  417.  685  0.179 -1.391 -0.131  0.763 -0.083  0.204   0.0727007357
    418. 

  418.  690  0.180 -1.390 -0.130  0.763 -0.084  0.204   0.0727005768
    419. 

  419.  692  0.180 -1.391 -0.130  0.763 -0.084  0.204   0.0727003955
    420. 

  420.  693  0.180 -1.391 -0.130  0.763 -0.083  0.204   0.0727003020
    421. 

  421.  711  0.178 -1.391 -0.130  0.763 -0.083  0.204   0.0726993645
    422. 

  422.  719  0.180 -1.391 -0.130  0.764 -0.084  0.207   0.0726991298
    423. 

  423.  720  0.179 -1.391 -0.130  0.763 -0.084  0.206   0.0726990916
    424. 

  424.  723  0.179 -1.391 -0.130  0.763 -0.084  0.206   0.0726990741
    425. 

  425.  725  0.179 -1.391 -0.130  0.763 -0.084  0.206   0.0726990063
    426. 

  426.  737  0.179 -1.391 -0.130  0.763 -0.084  0.205   0.0726982144
    427. 

  427.  749  0.177 -1.393 -0.126  0.761 -0.083  0.204   0.0726891825
    428. 

  428.  753  0.176 -1.393 -0.124  0.760 -0.083  0.204   0.0726887712
    429. 

  429.  754  0.177 -1.393 -0.125  0.760 -0.083  0.204   0.0726887335
    430. 

  430.  755  0.177 -1.393 -0.125  0.760 -0.083  0.204   0.0726887232
    431. 

  431.  768  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726861836
    432. 

  432.  772  0.178 -1.392 -0.124  0.760 -0.084  0.204   0.0726861621
    433. 

  433.  773  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726861545
    434. 

  434.  775  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726861539
    435. 

  435.  776  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726860383
    436. 

  436.  784  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726860034
    437. 

  437.  810  0.178 -1.392 -0.123  0.760 -0.085  0.204   0.0726859213
    438. 

  438.  821  0.178 -1.392 -0.123  0.760 -0.085  0.208   0.0726852144
    439. 

  439.  822  0.178 -1.392 -0.123  0.760 -0.085  0.206   0.0726851212
    440. 

  440.  824  0.178 -1.392 -0.123  0.760 -0.085  0.207   0.0726847545
    441. 

  441.  834  0.177 -1.392 -0.122  0.760 -0.085  0.207   0.0726839707
    442. 

  442.  855  0.178 -1.392 -0.121  0.760 -0.085  0.207   0.0726838584
    443. 

  443.  857  0.178 -1.392 -0.121  0.760 -0.085  0.207   0.0726838037
    444. 

  444.  860  0.178 -1.392 -0.121  0.760 -0.085  0.207   0.0726837988
    445. 

  445.  861  0.178 -1.392 -0.121  0.760 -0.085  0.207   0.0726837969
    446. 

  446.  863  0.178 -1.392 -0.121  0.760 -0.085  0.207   0.0726836686
    447. 

  447. Powell done niters = 9
    448. 

  448. Computing relative cost
    449. 

  449.  0  -25.0 -25.0 -25.0   1.006857
    450. 

  450.  1  -25.0 -25.0  25.0   1.044254
    451. 

  451.  2  -25.0  25.0 -25.0   1.029143
    452. 

  452.  3  -25.0  25.0  25.0   1.002896
    453. 

  453.  4   25.0 -25.0 -25.0   0.978538
    454. 

  454.  5   25.0 -25.0  25.0   1.013653
    455. 

  455.  6   25.0  25.0 -25.0   1.040085
    456. 

  456.  7   25.0  25.0  25.0   0.996926
    457. 

  457. REL:  8  0.072684    8.112353  1.014044 rel = 0.071677 
    458. 

  458. Number of iterations     9
    459. 

  459. Min cost was 0.072684
    460. 

  460. Number of FunctionCalls   867
    461. 

  461. TolPowell 0.000100
    462. 

  462. nMaxItersPowell 36
    463. 

  463. OptimizationTime 3.235000 sec
    464. 

  464. Parameters at optimum (transmm)  0.17782 -1.39207 -0.12115
    465. 

  465. Parameters at optimum (rotdeg)  0.75960 -0.08518  0.20712 
    466. 

  466. Final costs ----------------
    467. 

  467. Number of surface hits 2556
    468. 

  468. WM  Intensity    61.8206 +/-   9.0689
    469. 

  469. Ctx Intensity    78.7208 +/-   9.5066
    470. 

  470. Pct Contrast     24.2141 +/-  13.9696
    471. 

  471. Cost   0.0727
    472. 

  472. RelCost   0.3917
    473. 

  473. Reg at min cost was 
    474. 

  474.  0.996  -0.033  -0.078   0.022;
    475. 

  475.  0.080   0.081   0.994  -0.000;
    476. 

  476. -0.026  -0.996   0.083   0.179;
    477. 

  477.  0.000   0.000   0.000   1.000;
    478. 

  478. 

  479. Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat, type = 14 
    480. 

  480. Original Reg 
    481. 

  481.  0.997  -0.034  -0.074  -0.150;
    482. 

  482.  0.076   0.067   0.995   1.396;
    483. 

  483. -0.029  -0.997   0.070   0.282;
    484. 

  484.  0.000   0.000   0.000   1.000;
    485. 

  485. 

  486. Original Reg - Optimal Reg
    487. 

  487.  0.000  -0.001   0.004  -0.172;
    488. 

  488. -0.004  -0.013   0.001   1.396;
    489. 

  489. -0.002  -0.001  -0.013   0.103;
    490. 

  490.  0.000   0.000   0.000   0.000;
    491. 

  491. 

  492. Computing change in lh position
    493. 

  493. LH rmsDiffMean 1.774158
    494. 

  494. Computing change in rh position
    495. 

  495. Surface RMS Diff (mm) 1.670984 2.632894
    496. 

  496. mri_segreg done
    497. 

  497. mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
    498. 

  498. $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
    499. 

  499. setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
    500. 

  500. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/scripts
    501. 

  501. mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
    502. 

  502. sysname  Linux
    503. 

  503. hostname snake5
    504. 

  504. machine  x86_64
    505. 

  505. user     fkaule
    506. 

  506. movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/template.nii
    507. 

  507. regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/tmp.bbregister.7756/bbr.pass1.dat
    508. 

  508. subject sub004
    509. 

  509. dof 6
    510. 

  510. outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat
    511. 

  511. UseMask 0
    512. 

  512. UseLH 1
    513. 

  513. UseRH 1
    514. 

  514. nsubsamp 1
    515. 

  515. PenaltySign  -1
    516. 

  516. PenaltySlope 0.500000
    517. 

  517. PenaltyCenter 0.000000
    518. 

  518. surfname white
    519. 

  519. GMProjFrac 0.500000
    520. 

  520. WMProjAbs 2.000000
    521. 

  521. lhcostfile (null)
    522. 

  522. rhcostfile (null)
    523. 

  523. interp  trilinear (1)
    524. 

  524. frame  0
    525. 

  525. TolPowell 0.000000
    526. 

  526. nMaxItersPowell 36
    527. 

  527. n1dmin  3
    528. 

  528. Profile   0
    529. 

  529. Gdiag_no  -1
    530. 

  530. AddNoise  0 (0)
    531. 

  531. SynthSeed 1376849299
    532. 

  532. TransRandMax 0.000000
    533. 

  533. RotRandMax 0.000000
    534. 

  534. Translations 0.000000 0.000000 0.000000
    535. 

  535. Rotations   0.000000 0.000000 0.000000
    536. 

  536. Input reg
    537. 

  537.  0.996  -0.033  -0.078   0.022;
    538. 

  538.  0.080   0.081   0.994  -0.000;
    539. 

  539. -0.026  -0.996   0.083   0.179;
    540. 

  540.  0.000   0.000   0.000   1.000;
    541. 

  541. 

  542. Loading mov
    543. 

  543. Projecting LH Surfs
    544. 

  544. Loading lh.white surf
    545. 

  545. Loading lh.thickness for GM
    546. 

  546. GM Proj: 1 0.500000 2.000000
    547. 

  547. WM Proj: 0 0.500000 2.000000
    548. 

  548. Projecting RH Surfs
    549. 

  549. Loading rh.white surf
    550. 

  550. Loading rh.thickness
    551. 

  551. Projecting RH Surfs
    552. 

  552. Computing relative cost
    553. 

  553.  0  -25.0 -25.0 -25.0   1.004646
    554. 

  554.  1  -25.0 -25.0  25.0   1.013329
    555. 

  555.  2  -25.0  25.0 -25.0   1.015470
    556. 

  556.  3  -25.0  25.0  25.0   0.997744
    557. 

  557.  4   25.0 -25.0 -25.0   1.012491
    558. 

  558.  5   25.0 -25.0  25.0   1.013753
    559. 

  559.  6   25.0  25.0 -25.0   1.013924
    560. 

  560.  7   25.0  25.0  25.0   1.007717
    561. 

  561. REL:  8  0.095373    8.079073  1.009884 rel = 0.0944391 
    562. 

  562. Initial costs ----------------
    563. 

  563. Number of surface hits 254571
    564. 

  564. WM  Intensity    61.9760 +/-   9.7096
    565. 

  565. Ctx Intensity    78.5671 +/-   9.7566
    566. 

  566. Pct Contrast     23.8049 +/-  14.7579
    567. 

  567. Cost   0.0954
    568. 

  568. RelCost   0.0944
    569. 

  569. 

  570. ------------------------------------
    571. 

  571. Brute force preopt -0.1 0.1 0.1, n = 729
    572. 

  572.      0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0866   0.0866  0.0
    573. 

  573.      1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.0865   0.0865  0.0
    574. 

  574.      3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.0829   0.0829  0.0
    575. 

  575.      4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.0824   0.0824  0.0
    576. 

  576.      6  -0.1000  -0.1000  -0.1000  -0.1000   0.1000  -0.1000      0.0822   0.0822  0.0
    577. 

  577.      7  -0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.0000      0.0815   0.0815  0.0
    578. 

  578.     13  -0.1000  -0.1000  -0.1000   0.0000   0.0000   0.0000      0.0793   0.0793  0.0
    579. 

  579.     31  -0.1000  -0.1000   0.0000  -0.1000   0.0000   0.0000      0.0791   0.0791  0.0
    580. 

  580.     40  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.0000      0.0785   0.0785  0.0
    581. 

  581.     93  -0.1000   0.0000  -0.1000   0.0000   0.0000  -0.1000      0.0765   0.0765  0.0
    582. 

  582.     94  -0.1000   0.0000  -0.1000   0.0000   0.0000   0.0000      0.0762   0.0762  0.0
    583. 

  583.    120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.0757   0.0757  0.0
    584. 

  584.    121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0755   0.0755  0.0
    585. 

  585.    337   0.0000   0.0000  -0.1000   0.0000   0.0000   0.0000      0.0747   0.0747  0.0
    586. 

  586.    346   0.0000   0.0000  -0.1000   0.1000   0.0000   0.0000      0.0744   0.0744  0.0
    587. 

  587.    364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0727   0.0727  0.0
    588. 

  588. Brute Force --------------------------
    589. 

  589. Min cost was 0.072684
    590. 

  590. Number of iterations   729
    591. 

  591. Search time 2.098000 sec
    592. 

  592. Parameters at best (transmm, rotdeg)
    593. 

  593.   0.000   0.000   0.000  0.000  0.000  0.000 
    594. 

  594. --------------------------------------------
    595. 

  595. 

  596. Starting Powell Minimization
    597. 

  597. Init Powel Params dof = 6
    598. 

  598. 0 0
    599. 

  599. 1 0
    600. 

  600. 2 0
    601. 

  601. 3 0
    602. 

  602. 4 0
    603. 

  603. 5 0
    604. 

  604.    7  0.165  0.000  0.000  0.000  0.000  0.000   0.0933845584
    605. 

  605.    9  0.167  0.000  0.000  0.000  0.000  0.000   0.0933841782
    606. 

  606.   12  0.168  0.000  0.000  0.000  0.000  0.000   0.0933841401
    607. 

  607.   19  0.168 -0.054  0.000  0.000  0.000  0.000   0.0930159749
    608. 

  608.   20  0.168 -0.059  0.000  0.000  0.000  0.000   0.0930000867
    609. 

  609.   21  0.168 -0.080  0.000  0.000  0.000  0.000   0.0929866965
    610. 

  610.   23  0.168 -0.073  0.000  0.000  0.000  0.000   0.0929812374
    611. 

  611.   32  0.168 -0.073 -0.109  0.000  0.000  0.000   0.0913775735
    612. 

  612.   33  0.168 -0.073 -0.139  0.000  0.000  0.000   0.0912598531
    613. 

  613.   34  0.168 -0.073 -0.149  0.000  0.000  0.000   0.0912557191
    614. 

  614.   35  0.168 -0.073 -0.146  0.000  0.000  0.000   0.0912541483
    615. 

  615.   36  0.168 -0.073 -0.145  0.000  0.000  0.000   0.0912541193
    616. 

  616.   45  0.168 -0.073 -0.145 -0.009  0.000  0.000   0.0912387253
    617. 

  617.   46  0.168 -0.073 -0.145 -0.011  0.000  0.000   0.0912383717
    618. 

  618.   48  0.168 -0.073 -0.145 -0.010  0.000  0.000   0.0912383515
    619. 

  619.   55  0.168 -0.073 -0.145 -0.010 -0.057  0.000   0.0907298276
    620. 

  620.   56  0.168 -0.073 -0.145 -0.010 -0.075  0.000   0.0906906176
    621. 

  621.   66  0.168 -0.073 -0.145 -0.010 -0.075 -0.008   0.0906491432
    622. 

  622.   67  0.168 -0.073 -0.145 -0.010 -0.075 -0.034   0.0905906757
    623. 

  623.   68  0.168 -0.073 -0.145 -0.010 -0.075 -0.033   0.0905904571
    624. 

  624.   77  0.150 -0.073 -0.145 -0.010 -0.075 -0.033   0.0905518435
    625. 

  625.   89  0.150 -0.046 -0.145 -0.010 -0.075 -0.033   0.0904328796
    626. 

  626.   90  0.150 -0.041 -0.145 -0.010 -0.075 -0.033   0.0904259436
    627. 

  627.   91  0.150 -0.035 -0.145 -0.010 -0.075 -0.033   0.0904249695
    628. 

  628.   92  0.150 -0.037 -0.145 -0.010 -0.075 -0.033   0.0904248135
    629. 

  629.  101  0.150 -0.037 -0.143 -0.010 -0.075 -0.033   0.0904206539
    630. 

  630.  102  0.150 -0.037 -0.136 -0.010 -0.075 -0.033   0.0904164606
    631. 

  631.  104  0.150 -0.037 -0.138 -0.010 -0.075 -0.033   0.0904164075
    632. 

  632.  113  0.150 -0.037 -0.138 -0.006 -0.075 -0.033   0.0904161406
    633. 

  633.  114  0.150 -0.037 -0.138 -0.008 -0.075 -0.033   0.0904158820
    634. 

  634.  124  0.150 -0.037 -0.138 -0.008 -0.074 -0.033   0.0904157128
    635. 

  635.  133  0.150 -0.037 -0.138 -0.008 -0.074 -0.041   0.0904108071
    636. 

  636.  134  0.150 -0.037 -0.138 -0.008 -0.074 -0.040   0.0904104333
    637. 

  637.  143  0.146 -0.037 -0.138 -0.008 -0.074 -0.040   0.0904069638
    638. 

  638.  144  0.142 -0.037 -0.138 -0.008 -0.074 -0.040   0.0904052471
    639. 

  639.  164  0.142 -0.037 -0.139 -0.008 -0.074 -0.040   0.0904049513
    640. 

  640.  165  0.142 -0.037 -0.140 -0.008 -0.074 -0.040   0.0904048650
    641. 

  641.  186  0.142 -0.037 -0.140 -0.008 -0.073 -0.040   0.0904047886
    642. 

  642.  195  0.142 -0.037 -0.140 -0.008 -0.073 -0.045   0.0904041077
    643. 

  643.  196  0.142 -0.037 -0.140 -0.008 -0.073 -0.043   0.0904037585
    644. 

  644.  204  0.139 -0.037 -0.140 -0.008 -0.072 -0.044   0.0904032972
    645. 

  645.  205  0.140 -0.037 -0.140 -0.008 -0.072 -0.044   0.0904032652
    646. 

  646.  206  0.140 -0.037 -0.140 -0.008 -0.072 -0.044   0.0904032466
    647. 

  647.  241  0.140 -0.037 -0.139 -0.008 -0.072 -0.044   0.0904031320
    648. 

  648.  261  0.140 -0.037 -0.139 -0.008 -0.073 -0.044   0.0904030116
    649. 

  649.  269  0.140 -0.037 -0.139 -0.008 -0.073 -0.044   0.0904030093
    650. 

  650.  271  0.140 -0.037 -0.139 -0.008 -0.073 -0.044   0.0904029927
    651. 

  651.  273  0.140 -0.037 -0.139 -0.008 -0.073 -0.044   0.0904029889
    652. 

  652.  274  0.140 -0.037 -0.139 -0.008 -0.073 -0.044   0.0904029708
    653. 

  653.  285  0.140 -0.037 -0.139 -0.008 -0.073 -0.045   0.0904029541
    654. 

  654.  293  0.140 -0.038 -0.139 -0.008 -0.073 -0.045   0.0904029459
    655. 

  655.  313  0.140 -0.038 -0.139 -0.007 -0.073 -0.045   0.0904029052
    656. 

  656.  329  0.139 -0.038 -0.139 -0.007 -0.073 -0.045   0.0904028744
    657. 

  657.  332  0.139 -0.038 -0.139 -0.007 -0.073 -0.045   0.0904028657
    658. 

  658.  333  0.139 -0.038 -0.139 -0.007 -0.073 -0.045   0.0904028591
    659. 

  659.  365  0.139 -0.038 -0.140 -0.007 -0.073 -0.045   0.0904028467
    660. 

  660.  393  0.140 -0.038 -0.140 -0.007 -0.073 -0.045   0.0904028205
    661. 

  661.  401  0.140 -0.038 -0.140 -0.007 -0.073 -0.045   0.0904028168
    662. 

  662.  456  0.140 -0.038 -0.140 -0.007 -0.073 -0.045   0.0904027985
    663. 

  663. Powell done niters = 7
    664. 

  664. Computing relative cost
    665. 

  665.  0  -25.0 -25.0 -25.0   1.003687
    666. 

  666.  1  -25.0 -25.0  25.0   1.010969
    667. 

  667.  2  -25.0  25.0 -25.0   1.015503
    668. 

  668.  3  -25.0  25.0  25.0   0.996017
    669. 

  669.  4   25.0 -25.0 -25.0   1.011593
    670. 

  670.  5   25.0 -25.0  25.0   1.012373
    671. 

  671.  6   25.0  25.0 -25.0   1.013332
    672. 

  672.  7   25.0  25.0  25.0   1.008502
    673. 

  673. REL:  8  0.090403    8.071978  1.008997 rel = 0.0895967 
    674. 

  674. Number of iterations     7
    675. 

  675. Min cost was 0.090403
    676. 

  676. Number of FunctionCalls   525
    677. 

  677. TolPowell 0.000000
    678. 

  678. nMaxItersPowell 36
    679. 

  679. OptimizationTime 63.518000 sec
    680. 

  680. Parameters at optimum (transmm)  0.13977 -0.03823 -0.14024
    681. 

  681. Parameters at optimum (rotdeg) -0.00674 -0.07340 -0.04490 
    682. 

  682. Final costs ----------------
    683. 

  683. Number of surface hits 254571
    684. 

  684. WM  Intensity    61.9785 +/-   9.7235
    685. 

  685. Ctx Intensity    78.5620 +/-   9.7033
    686. 

  686. Pct Contrast     23.8028 +/-  14.6897
    687. 

  687. Cost   0.0904
    688. 

  688. RelCost   0.0944
    689. 

  689. Reg at min cost was 
    690. 

  690.  0.997  -0.031  -0.077   0.162;
    691. 

  691.  0.079   0.080   0.994  -0.039;
    692. 

  692. -0.025  -0.996   0.083   0.039;
    693. 

  693.  0.000   0.000   0.000   1.000;
    694. 

  694. 

  695. Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat, type = 14 
    696. 

  696. Original Reg 
    697. 

  697.  0.996  -0.033  -0.078   0.022;
    698. 

  698.  0.080   0.081   0.994  -0.000;
    699. 

  699. -0.026  -0.996   0.083   0.179;
    700. 

  700.  0.000   0.000   0.000   1.000;
    701. 

  701. 

  702. Original Reg - Optimal Reg
    703. 

  703. -0.000  -0.001  -0.001  -0.140;
    704. 

  704.  0.001   0.000  -0.000   0.038;
    705. 

  705. -0.001   0.000   0.000   0.140;
    706. 

  706.  0.000   0.000   0.000   0.000;
    707. 

  707. 

  708. Computing change in lh position
    709. 

  709. LH rmsDiffMean 0.238989
    710. 

  710. Computing change in rh position
    711. 

  711. Surface RMS Diff (mm) 0.221031 0.321591
    712. 

  712. mri_segreg done
    713. 

  713. tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.lta
    714. 

  714. tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
    715. 

  715. INFO: no target volume specified, assuming FreeSurfer orig volume.
    716. 

  716. target  volume orig
    717. 

  717. movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
    718. 

  718. reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat
    719. 

  719. LoadVol        0
    720. 

  720. ZeroCRAS       0
    721. 

  721. $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
    722. 

  722. Diagnostic Level -1
    723. 

  723. ---- Input registration matrix --------
    724. 

  724.  0.997  -0.031  -0.077   0.162;
    725. 

  725.  0.079   0.080   0.994  -0.039;
    726. 

  726. -0.025  -0.996   0.083   0.039;
    727. 

  727.  0.000   0.000   0.000   1.000;
    728. 

  728. float2int = 0
    729. 

  729. ---------------------------------------
    730. 

  730. INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig.mgz
    731. 

  731. Ttarg: --------------------
    732. 

  732. -1.000   0.000   0.000   128.000;
    733. 

  733.  0.000   0.000   1.000  -128.000;
    734. 

  734.  0.000  -1.000   0.000   128.000;
    735. 

  735.  0.000   0.000   0.000   1.000;
    736. 

  736. INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz
    737. 

  737. Tmov: --------------------
    738. 

  738. -0.700   0.000   0.000   95.893;
    739. 

  739.  0.000   0.000   0.667  -128.000;
    740. 

  740.  0.000  -0.667   0.000   128.000;
    741. 

  741.  0.000   0.000   0.000   1.000;
    742. 

  742. mkheaderreg = 0, float2int = 0
    743. 

  743. ---- Input registration matrix --------
    744. 

  744.  0.997  -0.031  -0.077   0.162;
    745. 

  745.  0.079   0.080   0.994  -0.039;
    746. 

  746. -0.025  -0.996   0.083   0.039;
    747. 

  747.  0.000   0.000   0.000   1.000;
    748. 

  748. Determinant 1
    749. 

  749. subject = sub004
    750. 

  750. RegMat ---------------------------
    751. 

  751.  0.997  -0.031  -0.077   0.162;
    752. 

  752.  0.079   0.080   0.994  -0.039;
    753. 

  753. -0.025  -0.996   0.083   0.039;
    754. 

  754.  0.000   0.000   0.000   1.000;
    755. 

  755. transformed matrix:
    756. 

  756.  1.000  -0.006   0.007  -0.048;
    757. 

  757.  0.006   1.000   0.009  -0.013;
    758. 

  758. -0.007  -0.009   1.000   0.261;
    759. 

  759.  0.000   0.000   0.000   1.000;
    760. 

  760. transformed matrix:
    761. 

  761.  0.698  -0.017  -0.053   45.936;
    762. 

  762. -0.054   0.055  -0.662   251.945;
    763. 

  763.  0.022   0.664   0.054  -12.768;
    764. 

  764.  0.000   0.000   0.000   1.000;
    765. 

  765. Cleaning up
    766. 

  766.  
    767. 

  767. Started at Thu Aug 8 21:37:12 CEST 2013 
    768. 

  768. Ended   at Thu Aug  8 21:50:01 CEST 2013
    769. 

  769. BBR-Run-Time-Sec 769
    770. 

  770.  
    771. 

  771. bbregister Done
    772. 

  772. To check results, run:
    773. 

  773. tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub004/mri/transforms/T2raw.dat --surf
    774.