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ImportT1MRI_without_manual_database_creation_prior

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Nov 22nd, 2018
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  1. darasan@imecas08:~$ singularity shell --bind /home/homeGlobal/darasan/sbr85:/mnt2,${morphologist_singularity_scripts}:/mnt3 ${morphologist_singularity_image}
  2. Singularity: Invoking an interactive shell within container...
  3.  
  4. Singularity brainvisa_4_6_0_xenial_updatedb_cmdline-2018-11-20-15fd7d8e3095.simg:~> bash /mnt3/import.sh /home/homeGlobal/darasan/test_subj 100206_1-T1w_acpc_dc_restore_1mm.nii.gz
  5. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100206_1-T1w_acpc_dc_restore_1mm
  6. DATABASE MOUNTED /mnt2
  7. SUBJECT NIFTI DIR MOUNTED /home/homeGlobal/darasan/test_subj
  8. SUBJECT NIFTI FILE NAME 100206_1-T1w_acpc_dc_restore_1mm.nii.gz
  9. SUBJECT NIFTI PREFIX 100206_1-T1w_acpc_dc_restore_1mm
  10. Loading toolbox cortical_surface
  11. Loading toolbox data management
  12. Loading toolbox datamind
  13. Loading toolbox freesurfer
  14. Loading toolbox morphologist
  15. Loading toolbox spm
  16. Loading toolbox structural_analysis
  17. Loading toolbox tools
  18. Loading toolbox viewers
  19. Loading toolbox My processes
  20. The log file for this session is
  21. '/home/homeGlobal/darasan/.brainvisa/brainvisa2.log'
  22. Headless Anatomist running in normal (non-headless) mode
  23. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  24.  
  25. Process Import T1 MRI started on 2018/11/22 07:49
  26. filein : /tmp/tmpsqBQ2M.nii.gz
  27. fileout : /mnt2/subjects/100206_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100206_1-T1w_acpc_dc_restore_1mm.nii.gz
  28. encoding: Binary
  29. normal : 0
  30. rescale : 1
  31. format :
  32. type : S16
  33. objtype :
  34. xdim : 0
  35. ydim : 0
  36. zdim : 0
  37. imin : default
  38. imax : default
  39. omin : 0
  40. omax : 4095
  41. reading /tmp/tmpsqBQ2M.nii.gz as Volume / FLOAT...
  42. reading done
  43. convert to Volume / S16
  44. converting data...
  45. convert done
  46. writing /mnt2/subjects/100206_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100206_1-T1w_acpc_dc_restore_1mm.nii.gz...
  47. done
  48. Process Import T1 MRI finished on 2018/11/22 07:49 (4 seconds)
  49. Singularity brainvisa_4_6_0_xenial_updatedb_cmdline-2018-11-20-15fd7d8e3095.simg:~> ls /mnt2
  50. subjects
  51. Singularity brainvisa_4_6_0_xenial_updatedb_cmdline-2018-11-20-15fd7d8e3095.simg:~> ls /mnt2/*
  52. 100206_1-T1w_acpc_dc_restore_1mm
  53. Singularity brainvisa_4_6_0_xenial_updatedb_cmdline-2018-11-20-15fd7d8e3095.simg:~> ls /mnt2/*/*
  54. t1mri
  55. Singularity brainvisa_4_6_0_xenial_updatedb_cmdline-2018-11-20-15fd7d8e3095.simg:~> ls /mnt2/*/*/*
  56. default_acquisition
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