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with_2_updates_one_after_create_one_after_import

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Dec 4th, 2018
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  1. darasan@imecas10:/data/Team_Caspers/Arasan$ bash import_update_morphologist.sh -s /data/Team_Caspers/Arasan/brainvisa_test/test_subjects_list.txt -d /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  2. MAKING DATABASE FOLDER /data/Team_Caspers/Arasan/brainvisa_test/sbr95 AS IT DOES NOT EXIST
  3. SINGULARITY IMAGE TO BE USED: /data/Team_Caspers/lmod/installed/brainvisa_extra/brainvisa_4_6_0_xenial_with_updatedb_createdb_added-2018-12-03-86a7458d4613.simg
  4. SPECIFIED DATABASE PATH: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  5. CREATING DATABASE: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  6. ############################################################## CREATING /mnt2
  7. Loading toolbox cortical_surface
  8. Loading toolbox data management
  9. Loading toolbox datamind
  10. Loading toolbox freesurfer
  11. Loading toolbox morphologist
  12. Loading toolbox spm
  13. Loading toolbox structural_analysis
  14. Loading toolbox tools
  15. Loading toolbox viewers
  16. Loading toolbox My processes
  17. The log file for this session is
  18. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  19. Headless Anatomist running in normal (non-headless) mode
  20. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  21.  
  22. Process Create database started on 2018/12/04 16:19
  23. /mnt2: parse directories and insert items
  24. /mnt2: 2 files are stored as 2 DiskItems in 0 seconds
  25. Generating database tables for /mnt2
  26. /mnt2: parse directories and insert items
  27. /mnt2: 2 files are stored as 2 DiskItems in 0 seconds
  28. Process Create database finished on 2018/12/04 16:19 (7 seconds)
  29. UPDATING DATABSE 1 : /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  30. ############################################################## UPDATING /mnt2
  31. Loading toolbox cortical_surface
  32. Loading toolbox data management
  33. Loading toolbox datamind
  34. Loading toolbox freesurfer
  35. Loading toolbox morphologist
  36. Loading toolbox spm
  37. Loading toolbox structural_analysis
  38. Loading toolbox tools
  39. Loading toolbox viewers
  40. Loading toolbox My processes
  41. The log file for this session is
  42. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  43. Database /mnt2 must be updated because there is no database file.
  44. Headless Anatomist running in normal (non-headless) mode
  45. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  46. WARNING: Cannot question database /mnt2. You should update this database.
  47.  
  48. Process Update databases started on 2018/12/04 16:19
  49. Generating database tables for /mnt2
  50. Clear database: /mnt2
  51. Update database: /mnt2
  52. /mnt2: parse directories and insert items
  53. /mnt2: 3 files are stored as 3 DiskItems in 0 seconds
  54. Process Update databases finished on 2018/12/04 16:19 (3 seconds)
  55. IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  56. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100408_1-T1w_acpc_dc_restore_1mm
  57. DATABASE MOUNTED /mnt2
  58. SUBJECT NIFTI DIR MOUNTED /mnt1
  59. SUBJECT NIFTI FILE NAME 100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  60. SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
  61. Loading toolbox cortical_surface
  62. Loading toolbox data management
  63. Loading toolbox datamind
  64. Loading toolbox freesurfer
  65. Loading toolbox morphologist
  66. Loading toolbox spm
  67. Loading toolbox structural_analysis
  68. Loading toolbox tools
  69. Loading toolbox viewers
  70. Loading toolbox My processes
  71. The log file for this session is
  72. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  73. Headless Anatomist running in normal (non-headless) mode
  74. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  75.  
  76. Process Import T1 MRI started on 2018/12/04 16:19
  77. filein : /tmp/tmpWsWszW.nii.gz
  78. fileout : /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  79. encoding: Binary
  80. normal : 0
  81. rescale : 1
  82. format :
  83. type : S16
  84. objtype :
  85. xdim : 0
  86. ydim : 0
  87. zdim : 0
  88. imin : default
  89. imax : default
  90. omin : 0
  91. omax : 4095
  92. reading /tmp/tmpWsWszW.nii.gz as Volume / FLOAT...
  93. reading done
  94. convert to Volume / S16
  95. converting data...
  96. convert done
  97. writing /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz...
  98. done
  99. Process Import T1 MRI finished on 2018/12/04 16:19 (3 seconds)
  100. IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  101. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100610_1-T1w_acpc_dc_restore_1mm
  102. DATABASE MOUNTED /mnt2
  103. SUBJECT NIFTI DIR MOUNTED /mnt1
  104. SUBJECT NIFTI FILE NAME 100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  105. SUBJECT NIFTI PREFIX 100610_1-T1w_acpc_dc_restore_1mm
  106. Loading toolbox cortical_surface
  107. Loading toolbox data management
  108. Loading toolbox datamind
  109. Loading toolbox freesurfer
  110. Loading toolbox morphologist
  111. Loading toolbox spm
  112. Loading toolbox structural_analysis
  113. Loading toolbox tools
  114. Loading toolbox viewers
  115. Loading toolbox My processes
  116. The log file for this session is
  117. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  118. Headless Anatomist running in normal (non-headless) mode
  119. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  120.  
  121. Process Import T1 MRI started on 2018/12/04 16:19
  122. filein : /tmp/tmpDXj8hB.nii.gz
  123. fileout : /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  124. encoding: Binary
  125. normal : 0
  126. rescale : 1
  127. format :
  128. type : S16
  129. objtype :
  130. xdim : 0
  131. ydim : 0
  132. zdim : 0
  133. imin : default
  134. imax : default
  135. omin : 0
  136. omax : 4095
  137. reading /tmp/tmpDXj8hB.nii.gz as Volume / FLOAT...
  138. reading done
  139. convert to Volume / S16
  140. converting data...
  141. convert done
  142. writing /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz...
  143. done
  144. Process Import T1 MRI finished on 2018/12/04 16:20 (4 seconds)
  145. UPDATING DATABSE 2: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  146. ############################################################## UPDATING /mnt2
  147. Loading toolbox cortical_surface
  148. Loading toolbox data management
  149. Loading toolbox datamind
  150. Loading toolbox freesurfer
  151. Loading toolbox morphologist
  152. Loading toolbox spm
  153. Loading toolbox structural_analysis
  154. Loading toolbox tools
  155. Loading toolbox viewers
  156. Loading toolbox My processes
  157. The log file for this session is
  158. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  159. Headless Anatomist running in normal (non-headless) mode
  160. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  161.  
  162. Process Update databases started on 2018/12/04 16:20
  163. Generating database tables for /mnt2
  164. Clear database: /mnt2
  165. Update database: /mnt2
  166. /mnt2: parse directories and insert items
  167. /mnt2: 12 files are stored as 12 DiskItems in 0 seconds
  168. Process Update databases finished on 2018/12/04 16:20 (6 seconds)
  169. MORPHOLOGIST SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  170. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MORPHOLOGIST 100408_1-T1w_acpc_dc_restore_1mm
  171. DATABASE MOUNTED /mnt2
  172. SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
  173. Loading toolbox cortical_surface
  174. Loading toolbox data management
  175. Loading toolbox datamind
  176. Loading toolbox freesurfer
  177. Loading toolbox morphologist
  178. Loading toolbox spm
  179. Loading toolbox structural_analysis
  180. Loading toolbox tools
  181. Loading toolbox viewers
  182. Loading toolbox My processes
  183. The log file for this session is
  184. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  185. Headless Anatomist running in normal (non-headless) mode
  186. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  187.  
  188. Process Check SPAM models installation started on 2018/12/04 16:20
  189. models: 6
  190. SPAM models are present.
  191. Process Check SPAM models installation finished on 2018/12/04 16:20 (0 seconds)
  192.  
  193. Process Morphologist 2015 started on 2018/12/04 16:20
  194. progress: 0.0 % ...
  195. progress: 0.0 % ...
  196. progress: 0.0 % ...
  197. progress: 0.0 % ...
  198. smoothing anatomy_data...
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