Python Query Examples

Example #1

File: cluster_recon_all.py Project: MadsJensen/ya_project

VERBOSE = True

import os
import sys
# import errno  # should do some error checking...
# import subprocess
# ENH: install "official" version of stormdb on isis/hyades
path_to_stormdb = '/users/cjb/src/git/cfin-tools/stormdb/stormdb'
sys.path.append(path_to_stormdb)

# change to stormdb.access (mod. __init__.py)
from access import Query

proj_code = 'MINDLAB2015_MR-YoungAddiction'

db = Query(proj_code)
proj_folder = os.path.join('/projects', proj_code)
scratch_folder = os.path.join(proj_folder, 'scratch')

recon_all_bin = '/opt/local/freesurfer-releases/5.3.0/bin/recon-all'
subjects_dir = os.path.join(scratch_folder, 'fs_subjects_dir')
script_dir = proj_folder+'/scripts/MR_scripts'

included_subjects = db.get_subjects()
# included_subjects = included_subjects[3:]
# just test with first one!
# included_subjects = [included_subjects[1]]

for sub in included_subjects:
    # this is an example of getting the DICOM files as a list
    sequence_name = 't1_mp2rage_sag_p2_iso_UNI_Images'

Example #2

File: maxfilter_demo.py Project: christellegans/pipelines

    proc = subprocess.Popen([command], shell=True)

    proc.communicate()
    return proc.returncode


proj_code = "MINDLAB2013_03-MEG-BlindPerception"
proj_path = "/projects/" + proj_code
analysis_name = "sss"

VERBOSE = True
FAKE = False  # NB
n_processes = 3  # Remember that each process is using n_threads cores by default!
n_threads = 2  # 2 threads per process

db = Query(proj_code=proj_code, verbose=True)

## Make copies of the binary, calibration and cross-talk correction files
## Place them e.g. in "proj_path"/misc/maxfilter

# cp /neuro/bin/util/x86_64-pc-linux-gnu/maxfilter-2.2.15 .
mx_cmd = proj_path + "/misc/maxfilter/maxfilter-2.2.15"
# cp /neuro/databases/sss/sss_cal.dat .
cal_db = proj_path + "/misc/maxfilter/sss_cal.dat"
# cp /neuro/databases/ctc/ct_sparse.fif .
ctc_db = proj_path + "/misc/maxfilter/ct_sparse.fif"

mf_params_defaults = {
    "input_file": None,
    "output_file": None,
    "autobad": "on",

Example #3

File: cluster_recon_all.py Project: sarathykousik/pipelines

import os, sys
import errno # should do some error checking...
import subprocess
# ENH: install "official" version of stormdb on isis/hyades
path_to_stormdb = '/users/cjb/src/git/cfin-tools/stormdb'
sys.path.append(path_to_stormdb)

# change to stormdb.access (mod. __init__.py)
from access import Query

import numpy as np

proj_code = 'MEG_EEG-Training'

db=Query(proj_code)
proj_folder = os.path.join('/projects', proj_code)
scratch_folder = os.path.join(proj_folder, 'scratch')

recon_all_bin = '/opt/local/freesurfer-releases/5.3.0/bin/recon-all'
subjects_dir = os.path.join(scratch_folder, 'fs_subjects_dir')
script_dir = proj_folder+'/scripts/mads_test_scripts'

included_subjects = db.get_subjects()
# just test with first one!
included_subjects = [included_subjects[0]]

for sub in included_subjects:

    # this is an example of getting the DICOM files as a list
    sequence_name='t1_mprage_3D_sag'

Example #4

File: maxfilter_demo.py Project: sarathykousik/pipelines

    proc = subprocess.Popen([command], shell=True)

    proc.communicate()
    return proc.returncode


proj_code = 'MINDLAB2013_03-MEG-BlindPerception'
proj_path = '/projects/' + proj_code
analysis_name = 'sss'

VERBOSE = True
FAKE = False  # NB
n_processes = 3  # Remember that each process is using n_threads cores by default!
n_threads = 2  # 2 threads per process

db = Query(proj_code=proj_code, verbose=True)

## Make copies of the binary, calibration and cross-talk correction files
## Place them e.g. in "proj_path"/misc/maxfilter

# cp /neuro/bin/util/x86_64-pc-linux-gnu/maxfilter-2.2.15 .
mx_cmd = proj_path + '/misc/maxfilter/maxfilter-2.2.15'
# cp /neuro/databases/sss/sss_cal.dat .
cal_db = proj_path + '/misc/maxfilter/sss_cal.dat'
# cp /neuro/databases/ctc/ct_sparse.fif .
ctc_db = proj_path + '/misc/maxfilter/ct_sparse.fif'

mf_params_defaults = {
    'input_file': None,
    'output_file': None,
    'autobad': 'on',