neurospin / unicog Goto Github PK

$ source /i2bm/local/Ubuntu-14.04-x86_64/brainvisa/bin/bv_env.sh
bash: /i2bm/local/Ubuntu-14.04-x86_64/brainvisa/bin/bv_env.sh: No such file or directory

Hi,

If you want to import a level session, how to modify the participants.tsv file:

1st proposition:
participant_id NIP acq_date
sub-1-ses-1 nip_number 2010-06-28
sub-1-ses-2 nip_number 2010-06-25
sub-2-ses-1 nip_number 2010-07-01
sub-2-ses-2 nip_number 2010-05-23

2nd proposition:
participant_id session NIP acq_date
sub-1 ses-1 nip_number 2010-06-28
sub-1 ses-2 nip_number 2010-06-25
sub-2 ses-1 nip_number 2010-07-01
sub-2 ses-2 nip_number 2010-05-23

I didn't see this kind of information in the Bids specification. Not sure if it possible to add a field in the participants.tsv ?

Any idea ?

Isa

Because neurospin_to_bids has moved, when launching python setup.py install, one gets:

error: fileerror: file '...//unicog/bids/neurospin_to_bids.py' does not exist

When importing longitudinal data (multiple sessions for each subject), neurospin_to_bids.py produces duplicate rows in participants.tsv, which is forbidden by BIDS:

Each participant MUST be described by one and only one row.

In file "import_and_convert_dicom.py" there is no possibility to choose the Prisma 3T scanner, only the TrioTim is used by default.

This is the error message I have:

python import_scans.py scan_list.txt
Reading scans list scan_list.txt
fetching scans
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/16
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/05
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/07
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/09
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/13
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/15
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/17
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/19
! WARNING: this path doesn't exist /neurospin/acquisition/database/TrioTim/20170221/lk160274*/23
Converting dicoms to nifti

Hello,

Working on my laptop, I first installed brainvisa, then run bv_env.sh.

Then I installed unicogfmri without problem it seems:

cp983411@is153352:~/code/unicog$ python setup.py install --user
/volatile/brainvisa-4.5.0/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'distname'
warnings.warn(msg)
running install
running bdist_egg
running egg_info
writing unicog.egg-info/PKG-INFO
writing top-level names to unicog.egg-info/top_level.txt
writing dependency_links to unicog.egg-info/dependency_links.txt
reading manifest file 'unicog.egg-info/SOURCES.txt'
writing manifest file 'unicog.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/unicogfmri
copying unicogfmri/init.py -> build/lib.linux-x86_64-2.7/unicogfmri
creating build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri
copying unicogfmri/utils_unicogfmri/init.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri
creating build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/import_data
copying unicogfmri/utils_unicogfmri/import_data/init.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/import_data
copying unicogfmri/utils_unicogfmri/import_data/import_and_convert_dicom.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/import_data
creating build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer
copying unicogfmri/utils_unicogfmri/viewer/init.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer
copying unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer
copying unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer_3D.py -> build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/unicogfmri
creating build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/init.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri
creating build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/import_data
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/import_data/init.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/import_data
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/import_data/import_and_convert_dicom.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/import_data
creating build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer/init.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer
copying build/lib.linux-x86_64-2.7/unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer_3D.py -> build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer
copying build/lib.linux-x86_64-2.7/unicogfmri/init.py -> build/bdist.linux-x86_64/egg/unicogfmri
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/import_data/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/import_data/import_and_convert_dicom.py to import_and_convert_dicom.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer.py to pyanatomist_viewer.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/utils_unicogfmri/viewer/pyanatomist_viewer_3D.py to pyanatomist_viewer_3D.pyc
byte-compiling build/bdist.linux-x86_64/egg/unicogfmri/init.py to init.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying unicog.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying unicog.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying unicog.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying unicog.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying unicog.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/unicog-0.1-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing unicog-0.1-py2.7.egg
removing '/home/cp983411/.local/lib/python2.7/site-packages/unicog-0.1-py2.7.egg' (and everything under it)
creating /home/cp983411/.local/lib/python2.7/site-packages/unicog-0.1-py2.7.egg
Extracting unicog-0.1-py2.7.egg to /home/cp983411/.local/lib/python2.7/site-packages
unicog 0.1 is already the active version in easy-install.pth
/home/cp983411/.local/lib/python2.7/site-packages/unicog-0.1-py2.7.egg
Processing dependencies for unicog==0.1
Finished processing dependencies for unicog==0.1

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I can import unicogfmri in python without problem:

cp983411@is153352:~/code/unicog/unicogfmri/utils_unicogfmri/viewer/tests$ python
Python 2.7.3 (default, Feb 27 2014, 19:58:35)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import unicogfmri

#######

But when trying to run a modified version of the view-contrasts.py scripts:

cp983411@is153352:~/code/unicog/unicogfmri/utils_unicogfmri/viewer/tests$ python view_contrasts-mirror-patterns.py

Traceback (most recent call last):
File "view_contrasts-mirror-patterns.py", line 27, in
from unicogfmri.utils_unicog.viewer import pyanatomist_viewer
ImportError: No module named utils_unicog.viewer