without_update_after_create

darasan@imecas10:/data/Team_Caspers/Arasan$ bash 2import_update_morphologist.sh -s /data/Team_Caspers/Arasan/brainvisa_test/test_subjects_list.txt -d /data/Team_Caspers/Arasan/brainvisa_test/sbr95
MAKING DATABASE FOLDER /data/Team_Caspers/Arasan/brainvisa_test/sbr95 AS IT DOES NOT EXIST
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
SPECIFIED DATABASE PATH: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
CREATING DATABASE: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
############################################################## CREATING /mnt2
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is
'/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py

Process Create database started on 2018/12/04 16:15
/mnt2: parse directories and insert items
/mnt2: 2 files are stored as 2 DiskItems in 0 seconds
Generating database tables for /mnt2
/mnt2: parse directories and insert items
/mnt2: 2 files are stored as 2 DiskItems in 0 seconds
Process Create database finished on 2018/12/04 16:15 (8 seconds)
IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100408_1-T1w_acpc_dc_restore_1mm
DATABASE MOUNTED /mnt2
SUBJECT NIFTI DIR MOUNTED /mnt1
SUBJECT NIFTI FILE NAME 100408_1-T1w_acpc_dc_restore_1mm.nii.gz
SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is
'/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
Database /mnt2 must be updated because there is no database file.
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
WARNING: Cannot question database /mnt2. You should update this database.
WARNING: Cannot question database /mnt2. You should update this database.
WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
update this database.
WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
update this database.

Process Import T1 MRI started on 2018/12/04 16:15
filein  : /tmp/tmpy6JRMm.nii.gz
fileout : /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
encoding: Binary
normal  : 0
rescale : 1
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : 0
omax    : 4095
reading /tmp/tmpy6JRMm.nii.gz as Volume / FLOAT...
reading done
convert to Volume / S16
converting data...
convert done
writing /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz...
done
Process Import T1 MRI finished on 2018/12/04 16:15 (5 seconds)
ERROR no such table: _FILENAMES_

--------------------------------------------------------------------------------
OperationalError
processes.py (3216) in _processExecution:

item, update=True)

sqlFSODatabase.py (278) in insertDiskItem:

self.insertDiskItems( ( item, ), **kwargs )

sqlFSODatabase.py (2020) in insertDiskItems:

insertParentDirs=insertParentDirs )

sqlFSODatabase.py (1127) in insertDiskItems:

diSet = self._diskItemsWithParents( diskItems )

sqlFSODatabase.py (1115) in _diskItemsWithParents:

( reldirname, ) ).fetchone()

ERROR no such table: _FILENAMES_

--------------------------------------------------------------------------------
OperationalError
processes.py (3216) in _processExecution:

item, update=True)

sqlFSODatabase.py (278) in insertDiskItem:

self.insertDiskItems( ( item, ), **kwargs )

sqlFSODatabase.py (2020) in insertDiskItems:

insertParentDirs=insertParentDirs )

sqlFSODatabase.py (1127) in insertDiskItems:

diSet = self._diskItemsWithParents( diskItems )

sqlFSODatabase.py (1115) in _diskItemsWithParents:

( reldirname, ) ).fetchone()

IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100610_1-T1w_acpc_dc_restore_1mm
DATABASE MOUNTED /mnt2
SUBJECT NIFTI DIR MOUNTED /mnt1
SUBJECT NIFTI FILE NAME 100610_1-T1w_acpc_dc_restore_1mm.nii.gz
SUBJECT NIFTI PREFIX 100610_1-T1w_acpc_dc_restore_1mm
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is
'/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
Database /mnt2 must be updated because there is no database file.
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
WARNING: Cannot question database /mnt2. You should update this database.
WARNING: Cannot question database /mnt2. You should update this database.
WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
update this database.
WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
update this database.

Process Import T1 MRI started on 2018/12/04 16:15
filein  : /tmp/tmpsE_qpS.nii.gz
fileout : /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
encoding: Binary
normal  : 0
rescale : 1
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : 0
omax    : 4095
reading /tmp/tmpsE_qpS.nii.gz as Volume / FLOAT...
reading done
convert to Volume / S16
converting data...
convert done
writing /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz...
done
Process Import T1 MRI finished on 2018/12/04 16:15 (4 seconds)
ERROR no such table: _FILENAMES_

--------------------------------------------------------------------------------
OperationalError
processes.py (3216) in _processExecution:

item, update=True)

sqlFSODatabase.py (278) in insertDiskItem:

self.insertDiskItems( ( item, ), **kwargs )

sqlFSODatabase.py (2020) in insertDiskItems:

insertParentDirs=insertParentDirs )

sqlFSODatabase.py (1127) in insertDiskItems:

diSet = self._diskItemsWithParents( diskItems )

sqlFSODatabase.py (1115) in _diskItemsWithParents:

( reldirname, ) ).fetchone()

ERROR no such table: _FILENAMES_

--------------------------------------------------------------------------------
OperationalError
processes.py (3216) in _processExecution:

item, update=True)

sqlFSODatabase.py (278) in insertDiskItem:

self.insertDiskItems( ( item, ), **kwargs )

sqlFSODatabase.py (2020) in insertDiskItems:

insertParentDirs=insertParentDirs )

sqlFSODatabase.py (1127) in insertDiskItems:

diSet = self._diskItemsWithParents( diskItems )

sqlFSODatabase.py (1115) in _diskItemsWithParents:

( reldirname, ) ).fetchone()

UPDATING DATABSE 2: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
############################################################## UPDATING /mnt2
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is
'/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
Database /mnt2 must be updated because there is no database file.
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
WARNING: Cannot question database /mnt2. You should update this database.

Process Update databases started on 2018/12/04 16:15
Generating database tables for /mnt2
Clear database: /mnt2
Update database: /mnt2
/mnt2: parse directories and insert items
/mnt2: 12 files are stored as 12 DiskItems in 0 seconds
Process Update databases finished on 2018/12/04 16:15 (3 seconds)
MORPHOLOGIST SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MORPHOLOGIST 100408_1-T1w_acpc_dc_restore_1mm
DATABASE MOUNTED /mnt2
SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is
'/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py

Process Check SPAM models installation started on 2018/12/04 16:16
models: 6
SPAM models are present.
Process Check SPAM models installation finished on 2018/12/04 16:16 (0 seconds)

Process Morphologist 2015 started on 2018/12/04 16:16
progress: 0.0 % ...
progress: 0.0 % ...
progress: 0.0 % ...
progress: 0.0 % ...
smoothing anatomy_data...