def prep_group_analysis_workflow(c, resource, subject_infos):
#
# this function runs once per output file during group analysis
#
# p_id = a list of pipeline IDs, i.e. the name of the output folder for
# the strat
# s_ids = a list of all the subject IDs
# scan_ids = a list of scan IDs
# s_paths = a list of all of the filepaths of this particular output
# file that prep_group_analysis_workflow is being called for
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
# set this to False for now
fTest = False
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] = []
order[h] = count
count += 1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
print '\n\nMeasure: ', measure, '\n\n'
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
print '\n\ncolumns[sub_id]: ', columns[sub_id], '\n\n'
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(
m_dict[sub][measure])
else:
raise Exception(
"Couldn't find %s value for subject %s"
% (measure, sub))
else:
raise Exception(
"Couldn't find subject %s in the parameter file"
% sub)
print '\n\ncolumns[measure]: ', columns, '\n\n'
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exists" % (mod_path)
new_phenotypic_file = os.path.join(mod_path,
os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
# END get_phenotypic_file function
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if 1 in c.runScrubbing:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+', s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',
s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print "Found Multiple threshold value "
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
if len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
import yaml
for config in c.modelConfigs:
print c.modelConfigs
print config
try:
conf = Configuration(yaml.load(open(os.path.realpath(config),
'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
group_sublist = open(conf.subject_list, 'r')
sublist_items = group_sublist.readlines()
subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
''' begin iteration through group subject list for processing '''
for sub in subject_list:
# let's check to make sure the subject list is formatted for
# repeated measures properly if repeated measures is enabled and
# vice versa
if (c.repeatedMeasures == True) and (',' not in sub):
print '\n\n'
print '[!] CPAC says: The group analysis subject list is ' \
'not inthe appropriate format for repeated ' \
'measures.\n'
print 'Please use the appropriate format as described in ' \
'the CPAC User Guide or turn off Repeated Measures ' \
'in the CPAC pipeline configuration editor, found ' \
'in the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'NOTE: CPAC generates a properly-formatted group ' \
'analysis subject list meant for running repeated ' \
'measures when you create your original subject ' \
'list. Look for \'subject_list_group_analysis_' \
'repeated_measures.txt\' in the directory where ' \
'you created your subject list.\n\n'
raise Exception
elif (c.repeatedMeasures == False) and (',' in sub):
print '\n\n'
print '[!] CPAC says: It looks like your group analysis ' \
'subject list is formatted for running repeated ' \
'measures, but \'Run Repeated Measures\' is not ' \
'enabled in the pipeline configuration, found in ' \
'the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'Double-check your pipeline configuration?\n\n'
raise Exception
''' process subject ids for repeated measures, if it is on '''
# if repeated measures is being run and the subject list
# is a list of subject IDs and scan IDs concatenated
if (c.repeatedMeasures == True):
# sub.count(',') equals 1 when there is either multiple scans
# or multiple sessions but not both, for repeated measures
# sub.count(',') equals 2 when there are multiple sessions
# AND scans, for repeated measures
if sub.count(',') == 1:
sub_id = sub.split(',', 1)[0]
other_id = sub.split(',', 1)[1]
elif sub.count(',') == 2:
sub_id = sub.split(',', 2)[0]
scan_id = sub.split(',', 2)[1]
session_id = sub.split(',', 2)[2]
''' drop subjects from the group subject list '''
# check the path files in path_files_here folder in the subject's
# output folder - and drop any subjects from the group analysis
# subject list which do not exist in the paths to the output files
for path in s_paths:
if (c.repeatedMeasures == True):
if sub.count(',') == 1:
if (sub_id in path) and (other_id in path):
exist_paths.append(sub)
elif sub.count(',') == 2:
if (sub_id in path) and (scan_id in path) and \
(session_id in path):
exist_paths.append(sub)
else:
if sub in path:
exist_paths.append(sub)
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) > 0:
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "..for derivatives:"
print resource
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
# create the path string for the group analysis output
out_dir = os.path.dirname(s_paths[0]).split(p_id[0] + '/')
out_dir = os.path.join(conf.output_dir, out_dir[1])
out_dir = out_dir.replace(
s_ids[0], 'group_analysis_results_%s/_grp_model_%s' %
(p_id[0], conf.model_name))
mod_path = os.path.join(out_dir, 'model_files')
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
''' write the new subject list '''
new_sub_file = os.path.join(mod_path,
os.path.basename(conf.subject_list))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >> f, sub
f.close()
except:
print "Error: Could not open subject list file: ", new_sub_file
raise Exception
conf.update('subject_list', new_sub_file)
sub_id = conf.subject_id_label
if measure_dict != None:
conf.update(
'pheno_file',
get_phenotypic_file(conf.pheno_file, measure_dict,
measure_list, mod_path, sub_id))
print 'conf updated pheno: ', conf.pheno_file, '\n\n'
print "Model config dictionary ->"
print conf.__dict__
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
''' get the motion statistics parameter file, if present '''
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
parameter_file = os.path.join(
c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv' %
(scan_ids[0].strip('_'), threshold_val))
if 1 in c.runGenerateMotionStatistics:
if not os.path.exists(parameter_file):
print '\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n'
print 'Path not found: ', parameter_file, '\n\n'
raise Exception
elif (1 not in c.runGenerateMotionStatistics) and (
os.path.exists(parameter_file)):
if not os.path.exists(parameter_file):
print '\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n'
print 'Path not found: ', parameter_file, '\n\n'
raise Exception
else:
def no_measures_error(measure):
print '\n\n[!] CPAC says: The measure %s was included in ' \
'your group analysis design matrix formula, but ' \
'Generate Motion Statistics was not run during ' \
'individual-level analysis.\n' % measure
print 'Please run Generate Motion Statistics if you wish ' \
'to include this measure in your model.\n'
print 'If you HAVE completed a run with this option ' \
'enabled, then you are seeing this error because ' \
'the motion parameter file normally created by this ' \
'option is missing.\n\n'
raise Exception
for measure in measure_list:
if (measure in conf.design_formula):
no_measures_error(measure)
parameter_file = None
''' run create_fsl_model.py to generate the group analysis models '''
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, p_id[0])
# the current output that cpac_group_analysis_pipeline.py and
# create_fsl_model.py is currently being run for
current_output = s_paths[0].replace(pipeline_path, '').split('/')[2]
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, fTest, parameter_file, pipeline_path,
current_output, True)
#print >>diag, "> Runs create_fsl_model."
#print >>diag, ""
except Exception, e:
print "FSL Group Analysis model not successfully created - error in create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append((conf.output_dir, conf.subject_list))
def configuration_strategy_mock(method='FSL'):
# mock the config dictionary
c = Configuration({
"num_ants_threads": 4,
"workingDirectory": "/scratch/pipeline_tests",
"crashLogDirectory": "/scratch",
"outputDirectory":
"/output/output/pipeline_analysis_nuisance/sub-M10978008_ses-NFB3",
"resolution_for_func_preproc": "3mm",
"resolution_for_func_derivative": "3mm",
"template_for_resample":
"/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz",
"template_brain_only_for_func":
"/usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz",
"template_skull_for_func":
"/usr/share/fsl/5.0/data/standard/MNI152_T1_${func_resolution}.nii.gz",
"identityMatrix": "/usr/share/fsl/5.0/etc/flirtsch/ident.mat",
"funcRegFSLinterpolation": "sinc",
"funcRegANTSinterpolation": "LanczosWindowedSinc"
})
if method == 'ANTS':
c.update('regOption', 'ANTS')
else:
c.update('regOption', 'FSL')
# mock the strategy
strat = Strategy()
resource_dict = {
"mean_functional":
os.path.join(
c.outputDirectory,
"mean_functional/sub-M10978008_ses-NFB3_task-test_bold_calc_tshift_resample_volreg_calc_tstat.nii.gz"
),
"motion_correct":
os.path.join(
c.outputDirectory,
"motion_correct/_scan_test/sub-M10978008_ses-NFB3_task-test_bold_calc_tshift_resample_volreg.nii.gz"
),
"anatomical_brain":
os.path.join(
c.outputDirectory,
"anatomical_brain/sub-M10978008_ses-NFB3_acq-ao_brain_resample.nii.gz"
),
"ants_initial_xfm":
os.path.join(
c.outputDirectory,
"ants_initial_xfm/transform0DerivedInitialMovingTranslation.mat"),
"ants_affine_xfm":
os.path.join(c.outputDirectory,
"ants_affine_xfm/transform2Affine.mat"),
"ants_rigid_xfm":
os.path.join(c.outputDirectory, "ants_rigid_xfm/transform1Rigid.mat"),
"anatomical_to_mni_linear_xfm":
os.path.join(
c.outputDirectory,
"anatomical_to_mni_linear_xfm/sub-M10978008_ses-NFB3_T1w_resample_calc_flirt.mat"
),
"functional_to_anat_linear_xfm":
os.path.join(
c.outputDirectory,
"functional_to_anat_linear_xfm/_scan_test/sub-M10978008_ses-NFB3_task-test_bold_calc_tshift_resample_volreg_calc_tstat_flirt.mat"
),
'ants_symm_warp_field':
os.path.join(
c.outputDirectory,
"anatomical_to_symmetric_mni_nonlinear_xfm/transform3Warp.nii.gz"),
'ants_symm_affine_xfm':
os.path.join(c.outputDirectory,
"ants_symmetric_affine_xfm/transform2Affine.mat"),
'ants_symm_rigid_xfm':
os.path.join(c.outputDirectory,
"ants_symmetric_rigid_xfm/transform1Rigid.mat"),
'ants_symm_initial_xfm':
os.path.join(
c.outputDirectory,
"ants_symmetric_initial_xfm/transform0DerivedInitialMovingTranslation.mat"
),
"dr_tempreg_maps_files": [
os.path.join(
'/scratch', 'resting_preproc_sub-M10978008_ses-NFB3_cpac105',
'temporal_dual_regression_0/_scan_test/_selector_CSF-2mmE-M_aC-WM-2mmE-DPC5_G-M_M-SDB_P-2/_spatial_map_PNAS_Smith09_rsn10_spatial_map_file_..cpac_templates..PNAS_Smith09_rsn10.nii.gz/split_raw_volumes/temp_reg_map_000{0}.nii.gz'
.format(n)) for n in range(10)
]
}
if method == 'ANTS':
resource_dict["anatomical_to_mni_nonlinear_xfm"] = os.path.join(
c.outputDirectory,
"anatomical_to_mni_nonlinear_xfm/transform3Warp.nii.gz")
else:
resource_dict["anatomical_to_mni_nonlinear_xfm"] = os.path.join(
c.outputDirectory,
"anatomical_to_mni_nonlinear_xfm/sub-M10978008_ses-NFB3_T1w_resample_fieldwarp.nii.gz"
)
file_node_num = 0
for resource, filepath in resource_dict.items():
strat.update_resource_pool(
{resource: file_node(filepath, file_node_num)})
strat.append_name(resource + '_0')
file_node_num += 1
templates_for_resampling = [
(c.resolution_for_func_preproc, c.template_brain_only_for_func,
'template_brain_for_func_preproc', 'resolution_for_func_preproc'),
(c.resolution_for_func_preproc, c.template_brain_only_for_func,
'template_skull_for_func_preproc', 'resolution_for_func_preproc')
]
for resolution, template, template_name, tag in templates_for_resampling:
resampled_template = pe.Node(Function(
input_names=['resolution', 'template', 'template_name', 'tag'],
output_names=['resampled_template'],
function=resolve_resolution,
as_module=True),
name='resampled_' + template_name)
resampled_template.inputs.resolution = resolution
resampled_template.inputs.template = template
resampled_template.inputs.template_name = template_name
resampled_template.inputs.tag = tag
strat.update_resource_pool(
{template_name: (resampled_template, 'resampled_template')})
strat.append_name('resampled_template_0')
return c, strat
def prep_group_analysis_workflow(c, resource, subject_infos):
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
#print "p_id -%s, s_ids -%s, scan_ids -%s, s_paths -%s" %(p_id, s_ids, scan_ids, s_paths)
'''
#diag = open(os.path.join('/home/data/Projects/CPAC_Regression_Test/2013-08-19-20_v0-3-1/fsl-model/2013-09-03', 'group_analysis_diagnostic.txt'), 'wt')
#for tup in subject_infos:
# print >>diag, list(tup)
#print >>diag, ""
#for tup in zip(*subject_infos):
# print >>diag, list(tup)
#print >>diag, ""
print >>diag, "Working variables passed from cpac_group_runner: "
print >>diag, ""
print >>diag, "Pipeline ID (p_id): ", p_id
print >>diag, "Subject IDs (s_ids): ", s_ids
print >>diag, "Scan IDs (scan_ids): ", scan_ids
print >>diag, "(s_paths): ", s_paths
print >>diag, ""
'''
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
#print "phenotypic_file, m_dict", phenotypic_file, m_dict
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] = []
order[h] = count
count += 1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(
m_dict[sub][measure])
else:
raise Exception(
"Couldn't find %s value for subject %s"
% (measure, sub))
else:
raise Exception(
"Couldn't find subject %s in the parameter file"
% sub)
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exists" % (mod_path)
new_phenotypic_file = os.path.join(mod_path,
os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if c.runScrubbing == 1:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+', s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',
s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print "Found Multiple threshold value "
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
#pick the right parameter file from the pipeline folder
#create a dictionary of subject and measures in measure_list
if c.runScrubbing == 1:
try:
parameter_file = os.path.join(
c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv' %
(scan_ids[0].strip('_'), threshold_val))
if os.path.exists(parameter_file):
import csv
measure_dict = {}
f = csv.DictReader(open(parameter_file, 'r'))
for line in f:
measure_map = {}
for m in measure_list:
if line.get(m):
measure_map[m] = line[m]
measure_dict[line['Subject']] = measure_map
else:
print "No file name %s found" % parameter_file
except Exception:
print "Exception while extracting parameters from movement file - %s" % (
parameter_file)
#print >>diag, "Begins to iterate over each config file listed here: ", c.modelConfigs
#print >>diag, ""
for config in c.modelConfigs:
import yaml
try:
conf = Configuration(yaml.load(open(os.path.realpath(config),
'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
#print >>diag, "Starting iteration for config: ", config
#print >>diag, ""
group_sublist = open(conf.subjectListFile, 'r')
sublist_items = group_sublist.readlines()
subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
#print >>diag, "Subject list run-through #1: ", subject_list
#print >>diag, ""
#subject_list = [line.rstrip('\r\n') for line in open(conf.subjectListFile, 'r') \
# if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
# check for missing subject for the derivative
#print >>diag, "> Iterates over subject_list - for each subject in the subject list, it iterates over the paths in s_paths."
#print >>diag, "> For each path, it checks if the current subject exists in this path, and then appends this subject to 'exist_paths' list."
#print >>diag, ""
for sub in subject_list:
for path in s_paths:
if sub in path:
exist_paths.append(sub)
#print >>diag, "Current status of exist_paths list: "
#print >>diag, exist_paths
#print >>diag, ""
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) > 0:
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "..for derivatives:"
print resource
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
#import warnings
#warnings.warn(msg)
mod_path = os.path.join(
os.path.dirname(s_paths[0]).replace(
s_ids[0],
'group_analysis_results/_grp_model_%s' % (conf.modelName)),
'model_files')
#print >>diag, "> Created mod_path variable: ", mod_path
#print >>diag, ""
print "basename: ", os.path.basename(conf.subjectListFile)
try:
os.makedirs(mod_path)
print "Creating directory:"
print mod_path
except:
print "Attempted to create directory, but path already exists:"
print mod_path
new_sub_file = os.path.join(mod_path,
os.path.basename(conf.subjectListFile))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >> f, sub
f.close()
#print >>diag, "> Created new subject list file: ", new_sub_file
#print >>diag, ""
#print >>diag, "> ..which is filled with the subjects from exist_paths"
#print >>diag, ""
except:
print "Error: Could not open subject list file: ", new_sub_file
raise Exception
#print >>diag, "> Updates the FSL model config's subject list file parameter from: ", conf.subjectListFile
conf.update('subjectListFile', new_sub_file)
#print >>diag, "> ..to new subject list file: ", conf.subjectListFile
#print >>diag, ""
sub_id = conf.subjectColumn
'''
print >>diag, "> If measure_dict is not empty, it updates the phenotypic file with these parameters: "
print >>diag, ""
print >>diag, "measure_dict: ", measure_dict
print >>diag, "measure_list: ", measure_list
print >>diag, "mod_path: ", mod_path
print >>diag, "sub_id: ", sub_id
print >>diag, ""
'''
if measure_dict != None:
conf.update(
'phenotypicFile',
get_phenotypic_file(conf.phenotypicFile, measure_dict,
measure_list, mod_path, sub_id))
print "Model config dictionary ->"
print conf.__dict__
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, c.fTest, True)
#print >>diag, "> Runs create_fsl_model."
#print >>diag, ""
except Exception, e:
print "FSL Group Analysis model not successfully created - error in create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append(
(conf.outputModelFilesDirectory, conf.subjectListFile))
print "model_sub_list ->", model_sub_list
'''
def prep_group_analysis_workflow(c, resource, subject_infos):
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
#print "p_id -%s, s_ids -%s, scan_ids -%s, s_paths -%s" %(p_id, s_ids, scan_ids, s_paths)
'''
#diag = open(os.path.join('/home/data/Projects/CPAC_Regression_Test/2013-08-19-20_v0-3-1/fsl-model/2013-09-03', 'group_analysis_diagnostic.txt'), 'wt')
#for tup in subject_infos:
# print >>diag, list(tup)
#print >>diag, ""
#for tup in zip(*subject_infos):
# print >>diag, list(tup)
#print >>diag, ""
print >>diag, "Working variables passed from cpac_group_runner: "
print >>diag, ""
print >>diag, "Pipeline ID (p_id): ", p_id
print >>diag, "Subject IDs (s_ids): ", s_ids
print >>diag, "Scan IDs (scan_ids): ", scan_ids
print >>diag, "(s_paths): ", s_paths
print >>diag, ""
'''
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
#print "phenotypic_file, m_dict", phenotypic_file, m_dict
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] =[]
order[h] = count
count+=1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(m_dict[sub][measure])
else:
raise Exception("Couldn't find %s value for subject %s"%(measure,sub))
else:
raise Exception("Couldn't find subject %s in the parameter file"%sub)
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exists"%(mod_path)
new_phenotypic_file = os.path.join(mod_path, os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if c.runScrubbing == 1:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print "Found Multiple threshold value "
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
#pick the right parameter file from the pipeline folder
#create a dictionary of subject and measures in measure_list
if c.runScrubbing == 1:
try:
parameter_file = os.path.join(c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv'%(scan_ids[0].strip('_'),threshold_val))
if os.path.exists(parameter_file):
import csv
measure_dict = {}
f = csv.DictReader(open(parameter_file,'r'))
for line in f:
measure_map = {}
for m in measure_list:
if line.get(m):
measure_map[m] = line[m]
measure_dict[line['Subject']] = measure_map
else:
print "No file name %s found"%parameter_file
except Exception:
print "Exception while extracting parameters from movement file - %s"%(parameter_file)
#print >>diag, "Begins to iterate over each config file listed here: ", c.modelConfigs
#print >>diag, ""
for config in c.modelConfigs:
import yaml
try:
conf = Configuration(yaml.load(open(os.path.realpath(config), 'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
#print >>diag, "Starting iteration for config: ", config
#print >>diag, ""
group_sublist = open(conf.subjectListFile, 'r')
sublist_items = group_sublist.readlines()
subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
#print >>diag, "Subject list run-through #1: ", subject_list
#print >>diag, ""
#subject_list = [line.rstrip('\r\n') for line in open(conf.subjectListFile, 'r') \
# if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
# check for missing subject for the derivative
#print >>diag, "> Iterates over subject_list - for each subject in the subject list, it iterates over the paths in s_paths."
#print >>diag, "> For each path, it checks if the current subject exists in this path, and then appends this subject to 'exist_paths' list."
#print >>diag, ""
for sub in subject_list :
for path in s_paths:
if sub in path:
exist_paths.append(sub)
#print >>diag, "Current status of exist_paths list: "
#print >>diag, exist_paths
#print >>diag, ""
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) >0:
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "..for derivatives:"
print resource
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
#import warnings
#warnings.warn(msg)
mod_path = os.path.join(os.path.dirname(s_paths[0]).replace(s_ids[0], 'group_analysis_results/_grp_model_%s'%(conf.modelName)),
'model_files')
#print >>diag, "> Created mod_path variable: ", mod_path
#print >>diag, ""
print "basename: ", os.path.basename(conf.subjectListFile)
try:
os.makedirs(mod_path)
print "Creating directory:"
print mod_path
except:
print "Attempted to create directory, but path already exists:"
print mod_path
new_sub_file = os.path.join(mod_path, os.path.basename(conf.subjectListFile))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >>f, sub
f.close()
#print >>diag, "> Created new subject list file: ", new_sub_file
#print >>diag, ""
#print >>diag, "> ..which is filled with the subjects from exist_paths"
#print >>diag, ""
except:
print "Error: Could not open subject list file: ", new_sub_file
raise Exception
#print >>diag, "> Updates the FSL model config's subject list file parameter from: ", conf.subjectListFile
conf.update('subjectListFile',new_sub_file)
#print >>diag, "> ..to new subject list file: ", conf.subjectListFile
#print >>diag, ""
sub_id = conf.subjectColumn
'''
print >>diag, "> If measure_dict is not empty, it updates the phenotypic file with these parameters: "
print >>diag, ""
print >>diag, "measure_dict: ", measure_dict
print >>diag, "measure_list: ", measure_list
print >>diag, "mod_path: ", mod_path
print >>diag, "sub_id: ", sub_id
print >>diag, ""
'''
if measure_dict != None:
conf.update('phenotypicFile',get_phenotypic_file(conf.phenotypicFile, measure_dict, measure_list, mod_path, sub_id))
print "Model config dictionary ->"
print conf.__dict__
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, c.fTest, True)
#print >>diag, "> Runs create_fsl_model."
#print >>diag, ""
except Exception, e:
print "FSL Group Analysis model not successfully created - error in create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append((conf.outputModelFilesDirectory, conf.subjectListFile))
print "model_sub_list ->", model_sub_list
'''
def prep_group_analysis_workflow(c, group_config_file, resource, subject_infos, threshold_val):
#
# this function runs once per output file during group analysis
#
import yaml
import commands
# p_id = a list of pipeline IDs, i.e. the name of the output folder for
# the strat
# s_ids = a list of all the subject IDs
# scan_ids = a list of scan IDs
# s_paths = a list of all of the filepaths of this particular output
# file that prep_group_analysis_workflow is being called for
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
try:
group_conf = Configuration(yaml.load(open(os.path.realpath(group_config_file), 'r')))
except Exception as e:
err_string = "\n\n[!] CPAC says: Could not read group model " \
"configuration YML file. Ensure you have read access " \
"for the file and that it is formatted properly.\n\n" \
"Configuration file: %s\n\nError details: %s" \
% (group_config_file, e)
raise Exception(err_string)
group_sublist_file = open(group_conf.subject_list, 'r')
group_sublist_items = group_sublist_file.readlines()
group_sublist = [line.rstrip('\n') for line in group_sublist_items \
if not (line == '\n') and not line.startswith('#')]
# list of subjects for which paths which DO exist
exist_paths = []
# paths to the actual derivatives for those subjects
derivative_paths = []
z_threshold = float(group_conf.z_threshold[0])
p_threshold = float(group_conf.p_threshold[0])
custom_confile = group_conf.custom_contrasts
if ((custom_confile == None) or (custom_confile == '') or \
("None" in custom_confile)):
if (len(group_conf.f_tests) == 0) or (group_conf.f_tests == None):
fTest = False
else:
fTest = True
else:
if not os.path.exists(custom_confile):
errmsg = "\n[!] CPAC says: You've specified a custom contrasts " \
".CSV file for your group model, but this file cannot " \
"be found. Please double-check the filepath you have " \
"entered.\n\nFilepath: %s\n\n" % custom_confile
raise Exception(errmsg)
evs = open(custom_confile, 'r').readline()
evs = evs.rstrip('\r\n').split(',')
count_ftests = 0
fTest = False
for ev in evs:
if "f_test" in ev:
count_ftests += 1
if count_ftests > 0:
fTest = True
''' begin iteration through group subject list for processing '''
print "Sorting through subject list to check for missing outputs " \
"for %s..\n" % resource
for ga_sub in group_sublist:
# Strip out carriage-return character if it is there
if ga_sub.endswith('\r'):
ga_sub = ga_sub.rstrip('\r')
# ga_sub = subject ID taken off the group analysis subject list
# let's check to make sure the subject list is formatted for
# repeated measures properly if repeated measures is enabled
# and vice versa
if (group_conf.repeated_measures == True) and (',' not in ga_sub):
print '\n\n'
print '[!] CPAC says: The group analysis subject list ' \
'is not in the appropriate format for repeated ' \
'measures.\n'
print 'Please use the appropriate format as described in ' \
'the CPAC User Guide or turn off Repeated Measures ' \
'in the CPAC pipeline configuration editor, found ' \
'in the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'NOTE: CPAC generates a properly-formatted group ' \
'analysis subject list meant for running repeated ' \
'measures when you create your original subject ' \
'list. Look for \'subject_list_group_analysis_' \
'repeated_measures.txt\' in the directory where ' \
'you created your subject list.\n\n'
raise Exception
elif (group_conf.repeated_measures == False) and (',' in ga_sub):
print '\n\n'
print '[!] CPAC says: It looks like your group analysis ' \
'subject list is formatted for running repeated ' \
'measures, but \'Run Repeated Measures\' is not ' \
'enabled in the pipeline configuration, found in ' \
'the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'Double-check your pipeline configuration?\n\n'
raise Exception
''' process subject ids for repeated measures, if it is on '''
# if repeated measures is being run and the subject list
# is a list of subject IDs and scan IDs concatenated
if (group_conf.repeated_measures == True):
# sub.count(',') equals 1 when there is either multiple scans
# or multiple sessions but not both, for repeated measures
# sub.count(',') equals 2 when there are multiple sessions
# AND scans, for repeated measures
if ga_sub.count(',') == 1:
sub_id = ga_sub.split(',',1)[0]
other_id = ga_sub.split(',',1)[1]
elif ga_sub.count(',') == 2:
sub_id = ga_sub.split(',',2)[0]
scan_id = ga_sub.split(',',2)[1]
session_id = ga_sub.split(',',2)[2]
''' drop subjects from the group subject list '''
# check the path files in path_files_here folder in the
# subject's output folder - and drop any subjects from the
# group analysis subject list which do not exist in the paths
# to the output files
'''
REVISIT THIS LATER to establish a potentially better way to
pull output paths (instead of path_files_here)
'''
for path in s_paths:
if (group_conf.repeated_measures == True):
if ga_sub.count(',') == 1:
if (sub_id in path) and (other_id in path):
exist_paths.append(ga_sub)
derivative_paths.append(path)
elif ga_sub.count(',') == 2:
if (sub_id in path) and (scan_id in path) and \
(session_id in path):
exist_paths.append(ga_sub)
derivative_paths.append(path)
else:
if ga_sub in path:
exist_paths.append(ga_sub)
derivative_paths.append(path)
# END subject-dropping!
if len(derivative_paths) == 0:
print '\n\n\n[!] CPAC says: None of the subjects listed in the ' \
'group analysis subject list were found to have outputs ' \
'produced by individual-level analysis.\n\nEnsure that ' \
'the subjects listed in your group analysis subject list ' \
'are the same as the ones included in the individual-' \
'level analysis you are running group-level analysis for.' \
'\n\n\n'
raise Exception
''' END subject list iteration '''
# check to see if any derivatives of subjects are missing
if len(list(set(group_sublist) - set(exist_paths))) >0:
print "List of outputs missing for subjects:"
print list(set(group_sublist) - set(exist_paths))
print "..for derivatives:"
print resource
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
# create the path string for the group analysis output
out_dir = os.path.dirname(s_paths[0]).split(p_id[0] + '/')
out_dir = os.path.join(group_conf.output_dir, out_dir[1])
out_dir = out_dir.replace(s_ids[0], 'group_analysis_results_%s/_grp_model_%s'%(p_id[0],group_conf.model_name))
model_out_dir = os.path.join(group_conf.output_dir, 'group_analysis_results_%s/_grp_model_%s'%(p_id[0],group_conf.model_name))
mod_path = os.path.join(out_dir, 'model_files')
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
''' write the new subject list '''
new_sub_file = os.path.join(mod_path, os.path.basename(group_conf.subject_list))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >>f, sub
f.close()
except:
print "Error: Could not open subject list file: ", new_sub_file
raise Exception
group_conf.update('subject_list',new_sub_file)
sub_id_label = group_conf.subject_id_label
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
''' get the motion statistics parameter file, if present '''
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
for measure in measure_list:
if (measure in group_conf.design_formula):
parameter_file = os.path.join(c.outputDirectory, p_id[0], '%s%s_all_params.csv'%(scan_ids[0].strip('_'),threshold_val))
if 1 in c.runGenerateMotionStatistics:
if not os.path.exists(parameter_file):
print '\n\n[!] CPAC says: Could not find or open the motion ' \
'parameter file. This is necessary if you have included ' \
'any of the MeanFD measures in your group model.\n\n' \
'If Generate Motion Statistics is enabled, this file can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs. If it is not there, ' \
'double-check to see if individual-level analysis had ' \
'completed successfully.\n'
print 'Path not found: ', parameter_file, '\n\n'
raise Exception
else:
def no_measures_error(measure):
print '\n\n[!] CPAC says: The measure %s was included in ' \
'your group analysis design matrix formula, but ' \
'Generate Motion Statistics was not run during ' \
'individual-level analysis.\n' % measure
print 'Please run Generate Motion Statistics if you wish ' \
'to include this measure in your model.\n'
print 'If you HAVE completed a run with this option ' \
'enabled, then you are seeing this error because ' \
'the motion parameter file normally created by this ' \
'option is missing.\n\n'
raise Exception
for measure in measure_list:
if (measure in group_conf.design_formula):
no_measures_error(measure)
parameter_file = None
break
else:
parameter_file = None
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, p_id[0])
# the current output that cpac_group_analysis_pipeline.py and
# create_fsl_model.py is currently being run for
current_output = resource #s_paths[0].replace(pipeline_path, '').split('/')[2]
# generate working directory for this output's group analysis run
workDir = '%s/group_analysis/%s/%s_%s' % (c.workingDirectory, group_conf.model_name, resource, scan_ids[0])
# s_paths is a list of paths to each subject's derivative (of the current
# derivative gpa is being run on) - s_paths_dirList is a list of each directory
# in this path separated into list elements
# this makes strgy_path basically the directory path of the folders after
# the scan ID folder level
strgy_path = os.path.dirname(s_paths[0]).split(scan_ids[0])[1]
# get rid of periods in the path
for ch in ['.']:
if ch in strgy_path:
strgy_path = strgy_path.replace(ch, "")
# create nipype-workflow-name-friendly strgy_path
# (remove special characters)
strgy_path_name = strgy_path.replace('/', "_")
workDir = workDir + '/' + strgy_path_name
''' merge the remaining subjects for this current output '''
# then, take the group mask, and iterate over the list of subjects
# remaining to extract the mean of each subject using the group
# mask
merge_input = " "
merge_output_dir = workDir + "/merged_files"
if not os.path.exists(merge_output_dir):
os.makedirs(merge_output_dir)
merge_output = merge_output_dir + "/" + current_output + "_merged.nii.gz"
merge_mask_output = merge_output_dir + "/" + current_output + "_merged_mask.nii.gz"
# create a string per derivative filled with every subject's path to the
# derivative output file
for derivative_path in derivative_paths:
merge_input = merge_input + " " + derivative_path
merge_string = "fslmerge -t %s %s" % (merge_output, merge_input)
# MERGE the remaining outputs
try:
commands.getoutput(merge_string)
except Exception as e:
print "[!] CPAC says: FSL Merge failed for output: %s" % current_output
print "Error details: %s\n\n" % e
raise
merge_mask_string = "fslmaths %s -abs -Tmin -bin %s" % (merge_output, merge_mask_output)
# CREATE A MASK of the merged file
try:
commands.getoutput(merge_mask_string)
except Exception as e:
print "[!] CPAC says: FSL Mask failed for output: %s" % current_output
print "Error details: %s\n\n" % e
raise
derivative_means_dict = {}
roi_means_dict = {}
# CALCULATE THE MEANS of each remaining output using the group mask
for derivative_path in derivative_paths:
try:
if "Group Mask" in group_conf.mean_mask:
maskave_output = commands.getoutput("3dmaskave -mask %s %s" % (merge_mask_output, derivative_path))
elif "Individual Mask" in group_conf.mean_mask:
maskave_output = commands.getoutput("3dmaskave -mask %s %s" % (derivative_path, derivative_path))
except Exception as e:
print "[!] CPAC says: AFNI 3dmaskave failed for output: %s\n" \
"(Measure Mean calculation)" % current_output
print "Error details: %s\n\n" % e
raise
# get the subject ID of the current derivative path reliably
derivative_path_subID = derivative_path.replace(pipeline_path,"").strip("/").split("/")[0]
# this crazy-looking command simply extracts the mean from the
# verbose AFNI 3dmaskave output string
derivative_means_dict[derivative_path_subID] = maskave_output.split("\n")[-1].split(" ")[0]
# derivative_means_dict is now something like this:
# { 'sub001': 0.3124, 'sub002': 0.2981, .. }
# if custom ROI means are included in the model, do the same for those
if "Custom_ROI_Mean" in group_conf.design_formula:
try:
if "centrality" in derivative_path:
# resample custom roi mask to 3mm, then use that
resampled_roi_mask = merge_output_dir + "/" + current_output + "_resampled_roi_mask.nii.gz"
commands.getoutput("flirt -in %s -ref %s -o %s -applyxfm -init %s -interp nearestneighbour" % (group_conf.custom_roi_mask, derivative_path, resampled_roi_mask, c.identityMatrix))
ROIstats_output = commands.getoutput("3dROIstats -mask %s %s" % (resampled_roi_mask, derivative_path))
else:
ROIstats_output = commands.getoutput("3dROIstats -mask %s %s" % (group_conf.custom_roi_mask, derivative_path))
except Exception as e:
print "[!] CPAC says: AFNI 3dROIstats failed for output: %s" \
"\n(Custom ROI Mean calculation)" % current_output
print "Error details: %s\n\n" % e
raise
ROIstats_list = ROIstats_output.split("\t")
# calculate the number of ROIs - 3dROIstats output can be split
# into a list, and the actual ROI means begin at a certain point
num_rois = (len(ROIstats_list)-3)/2
roi_means = []
# create a list of the ROI means - each derivative of each subject
# will have N number of ROIs depending on how many ROIs were
# specified in the custom ROI mask
for num in range(num_rois+3,len(ROIstats_list)):
roi_means.append(ROIstats_list[num])
roi_means_dict[derivative_path_subID] = roi_means
else:
roi_means_dict = None
if len(derivative_means_dict.keys()) == 0:
err_string = "[!] CPAC says: Something went wrong with the " \
"calculation of the output means via the group mask.\n\n"
raise Exception(err_string)
''' run create_fsl_model.py to generate the group analysis models '''
from CPAC.utils import create_fsl_model
create_fsl_model.run(group_conf, fTest, parameter_file, derivative_means_dict, pipeline_path, current_output, model_out_dir, roi_means_dict, True)
''' begin GA workflow setup '''
if not os.path.exists(new_sub_file):
raise Exception("path to input subject list %s is invalid" % new_sub_file)
#if c.mixedScanAnalysis == True:
# wf = pe.Workflow(name = 'group_analysis/%s/grp_model_%s'%(resource, os.path.basename(model)))
#else:
wf = pe.Workflow(name = resource)
wf.base_dir = workDir
wf.config['execution'] = {'hash_method': 'timestamp', 'crashdump_dir': os.path.abspath(c.crashLogDirectory)}
log_dir = os.path.join(group_conf.output_dir, 'logs', 'group_analysis', resource, 'model_%s' % (group_conf.model_name))
if not os.path.exists(log_dir):
os.makedirs(log_dir)
else:
pass
# gp_flow
# Extracts the model files (.con, .grp, .mat, .fts) from the model
# directory and sends them to the create_group_analysis workflow gpa_wf
gp_flow = create_grp_analysis_dataflow("gp_dataflow_%s" % resource)
gp_flow.inputs.inputspec.grp_model = os.path.join(model_out_dir, "model_files", current_output)
gp_flow.inputs.inputspec.model_name = group_conf.model_name
gp_flow.inputs.inputspec.ftest = fTest
# gpa_wf
# Creates the actual group analysis workflow
gpa_wf = create_group_analysis(fTest, "gp_analysis_%s" % resource)
gpa_wf.inputs.inputspec.merged_file = merge_output
gpa_wf.inputs.inputspec.merge_mask = merge_mask_output
gpa_wf.inputs.inputspec.z_threshold = z_threshold
gpa_wf.inputs.inputspec.p_threshold = p_threshold
gpa_wf.inputs.inputspec.parameters = (c.FSLDIR, 'MNI152')
wf.connect(gp_flow, 'outputspec.mat',
gpa_wf, 'inputspec.mat_file')
wf.connect(gp_flow, 'outputspec.con',
gpa_wf, 'inputspec.con_file')
wf.connect(gp_flow, 'outputspec.grp',
gpa_wf, 'inputspec.grp_file')
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
gpa_wf, 'inputspec.fts_file')
# ds
# Creates the datasink node for group analysis
ds = pe.Node(nio.DataSink(), name='gpa_sink')
if 'sca_roi' in resource:
out_dir = os.path.join(out_dir, \
re.search('sca_roi_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(s_paths[0]))[0])[0]).group(0))
if 'dr_tempreg_maps_zstat_files_to_standard_smooth' in resource:
out_dir = os.path.join(out_dir, \
re.search('temp_reg_map_z_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(s_paths[0]))[0])[0]).group(0))
if 'centrality' in resource:
names = ['degree_centrality_binarize', 'degree_centrality_weighted', \
'eigenvector_centrality_binarize', 'eigenvector_centrality_weighted', \
'lfcd_binarize', 'lfcd_weighted']
for name in names:
if name in os.path.basename(s_paths[0]):
out_dir = os.path.join(out_dir, name)
break
if 'tempreg_maps' in resource:
out_dir = os.path.join(out_dir, \
re.search('\w*[#]*\d+', os.path.splitext(os.path.splitext(os.path.basename(s_paths[0]))[0])[0]).group(0))
# if c.mixedScanAnalysis == True:
# out_dir = re.sub(r'(\w)*scan_(\w)*(\d)*(\w)*[/]', '', out_dir)
ds.inputs.base_directory = out_dir
ds.inputs.container = ''
ds.inputs.regexp_substitutions = [(r'(?<=rendered)(.)*[/]','/'),
(r'(?<=model_files)(.)*[/]','/'),
(r'(?<=merged)(.)*[/]','/'),
(r'(?<=stats/clusterMap)(.)*[/]','/'),
(r'(?<=stats/unthreshold)(.)*[/]','/'),
(r'(?<=stats/threshold)(.)*[/]','/'),
(r'_cluster(.)*[/]',''),
(r'_slicer(.)*[/]',''),
(r'_overlay(.)*[/]','')]
'''
if 1 in c.runSymbolicLinks:
link_node = pe.MapNode(interface=util.Function(
input_names=['in_file',
'resource'],
output_names=[],
function=prepare_gp_links),
name='link_gp_', iterfield=['in_file'])
link_node.inputs.resource = resource
wf.connect(ds, 'out_file', link_node, 'in_file')
'''
########datasink connections#########
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
ds, 'model_files.@0')
wf.connect(gp_flow, 'outputspec.mat',
ds, 'model_files.@1' )
wf.connect(gp_flow, 'outputspec.con',
ds, 'model_files.@2')
wf.connect(gp_flow, 'outputspec.grp',
ds, 'model_files.@3')
wf.connect(gpa_wf, 'outputspec.merged',
ds, 'merged')
wf.connect(gpa_wf, 'outputspec.zstats',
ds, 'stats.unthreshold')
wf.connect(gpa_wf, 'outputspec.zfstats',
ds,'stats.unthreshold.@01')
wf.connect(gpa_wf, 'outputspec.fstats',
ds,'stats.unthreshold.@02')
wf.connect(gpa_wf, 'outputspec.cluster_threshold_zf',
ds, 'stats.threshold')
wf.connect(gpa_wf, 'outputspec.cluster_index_zf',
ds,'stats.clusterMap')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt_zf',
ds, 'stats.clusterMap.@01')
wf.connect(gpa_wf, 'outputspec.overlay_threshold_zf',
ds, 'rendered')
wf.connect(gpa_wf, 'outputspec.rendered_image_zf',
ds, 'rendered.@01')
wf.connect(gpa_wf, 'outputspec.cluster_threshold',
ds, 'stats.threshold.@01')
wf.connect(gpa_wf, 'outputspec.cluster_index',
ds, 'stats.clusterMap.@02')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt',
ds, 'stats.clusterMap.@03')
wf.connect(gpa_wf, 'outputspec.overlay_threshold',
ds, 'rendered.@02')
wf.connect(gpa_wf, 'outputspec.rendered_image',
ds, 'rendered.@03')
######################################
# Run the actual group analysis workflow
wf.run()
'''
except:
print "Error: Group analysis workflow run command did not complete successfully."
print "subcount: ", subcount
print "pathcount: ", pathcount
print "sublist: ", sublist_items
print "input subject list: "
print "conf: ", conf.subjectListFile
raise Exception
'''
print "**Workflow finished for model %s and resource %s"%(os.path.basename(group_conf.output_dir), resource)
def prep_group_analysis_workflow(model_df, pipeline_config_obj, \
model_name, group_config_obj, resource_id, preproc_strat, \
series_or_repeated_label):
#
# this function runs once per derivative type and preproc strat combo
# during group analysis
#
import os
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
pipeline_ID = pipeline_config_obj.pipeline_name
# get thresholds
z_threshold = float(group_config_obj.z_threshold[0])
p_threshold = float(group_config_obj.p_threshold[0])
sub_id_label = group_config_obj.subject_id_label
# determine if f-tests are included or not
custom_confile = group_config_obj.custom_contrasts
if ((custom_confile == None) or (custom_confile == '') or \
("None" in custom_confile) or ("none" in custom_confile)):
if (len(group_config_obj.f_tests) == 0) or \
(group_config_obj.f_tests == None):
fTest = False
else:
fTest = True
else:
if not os.path.exists(custom_confile):
errmsg = "\n[!] CPAC says: You've specified a custom contrasts " \
".CSV file for your group model, but this file cannot " \
"be found. Please double-check the filepath you have " \
"entered.\n\nFilepath: %s\n\n" % custom_confile
raise Exception(errmsg)
with open(custom_confile, "r") as f:
evs = f.readline()
evs = evs.rstrip('\r\n').split(',')
count_ftests = 0
fTest = False
for ev in evs:
if "f_test" in ev:
count_ftests += 1
if count_ftests > 0:
fTest = True
# create path for output directory
out_dir = os.path.join(group_config_obj.output_dir, \
"group_analysis_results_%s" % pipeline_ID, \
"group_model_%s" % model_name, resource_id, \
series_or_repeated_label, preproc_strat)
model_path = os.path.join(out_dir, 'model_files')
# generate working directory for this output's group analysis run
work_dir = os.path.join(c.workingDirectory, "group_analysis", model_name,\
resource_id, series_or_repeated_label, preproc_strat)
log_dir = os.path.join(out_dir, 'logs', resource_id, \
'model_%s' % model_name)
# create the actual directories
if not os.path.isdir(model_path):
try:
os.makedirs(model_path)
except Exception as e:
err = "\n\n[!] Could not create the group analysis output " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
if not os.path.isdir(work_dir):
try:
os.makedirs(work_dir)
except Exception as e:
err = "\n\n[!] Could not create the group analysis working " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
if not os.path.isdir(log_dir):
try:
os.makedirs(log_dir)
except Exception as e:
err = "\n\n[!] Could not create the group analysis logfile " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
# create new subject list based on which subjects are left after checking
# for missing outputs
new_participant_list = []
for part in list(model_df["Participant"]):
# do this instead of using "set" just in case, to preserve order
# only reason there may be duplicates is because of multiple-series
# repeated measures runs
if part not in new_participant_list:
new_participant_list.append(part)
new_sub_file = write_new_sub_file(model_path, \
group_config_obj.participant_list, \
new_participant_list)
group_conf.update('participant_list', new_sub_file)
# start processing the dataframe further
design_formula = group_config_obj.design_formula
# demean the motion params
if ("MeanFD" in design_formula) or ("MeanDVARS" in design_formula):
params = ["MeanFD_Power", "MeanFD_Jenkinson", "MeanDVARS"]
for param in params:
model_df[param] = model_df[param].astype(float)
model_df[param] = model_df[param].sub(model_df[param].mean())
# create 4D merged copefile, in the correct order, identical to design
# matrix
merge_outfile = model_name + "_" + resource_id + "_merged.nii.gz"
merge_outfile = os.path.join(model_path, merge_outfile)
merge_file = create_merged_copefile(list(model_df["Filepath"]), \
merge_outfile)
# create merged group mask
if group_config_obj.mean_mask[0] == "Group Mask":
merge_mask_outfile = os.path.basename(merge_file) + "_mask.nii.gz"
merge_mask = create_merged_mask(merge_file, merge_mask_outfile)
# calculate measure means, and demean
if "Measure_Mean" in design_formula:
model_df = calculate_measure_mean_in_df(model_df, merge_mask)
# calculate custom ROIs, and demean (in workflow?)
if "Custom_ROI_Mean" in design_formula:
custom_roi_mask = group_config_obj.custom_roi_mask
if (custom_roi_mask == None) or (custom_roi_mask == "None") or \
(custom_roi_mask == "none") or (custom_roi_mask == ""):
err = "\n\n[!] You included 'Custom_ROI_Mean' in your design " \
"formula, but you didn't supply a custom ROI mask file." \
"\n\nDesign formula: %s\n\n" % design_formula
raise Exception(err)
# make sure the custom ROI mask file is the same resolution as the
# output files - if not, resample and warn the user
roi_mask = check_mask_file_resolution(list(model_df["Raw_Filepath"])[0], \
custom_roi_mask, model_path, \
resource_id)
# if using group merged mask, trim the custom ROI mask to be within
# its constraints
if merge_mask:
output_mask = os.path.join(model_path, "group_masked_%s" \
% os.path.basename(input_mask))
roi_mask = trim_mask(roi_mask, merge_mask, output_mask)
# calculate
model_df = calculate_custom_roi_mean_in_df(model_df, roi_mask)
# modeling group variances separately
# add repeated measures 1's matrices
# patsify model DF, drop columns not in design formula
# process contrasts
wf = pe.Workflow(name=resource_id)
wf.base_dir = work_dir
crash_dir = os.path.join(pipeline_config_obj.crashLogDirectory, \
"group_analysis", model_name)
wf.config['execution'] = {'hash_method': 'timestamp', \
'crashdump_dir': crash_dir}
if "Measure_Mean" in design_formula:
measure_mean = pe.Node(util.Function(
input_names=['model_df', 'merge_mask'],
output_names=['model_df'],
function=calculate_measure_mean_in_df),
name='measure_mean')
measure_mean.inputs.model_df = model_df
wf.connect(merge_mask, "out_file", measure_mean, "merge_mask")
if "Custom_ROI_Mean" in design_formula:
roi_mean = pe.Node(util.Function())
group_config_obj.custom_roi_mask
#----------------
import yaml
import pandas as pd
# load group analysis model configuration file
try:
with open(os.path.realpath(group_config_file), "r") as f:
group_conf = Configuration(yaml.load(f))
except Exception as e:
err_string = "\n\n[!] CPAC says: Could not read group model " \
"configuration YML file. Ensure you have read access " \
"for the file and that it is formatted properly.\n\n" \
"Configuration file: %s\n\nError details: %s" \
% (group_config_file, e)
raise Exception(err_string)
# gather all of the information
# - lists of all the participant unique IDs (participant_site_session) and
# of all of the series IDs present in output_file_list
# - also returns the pipeline ID
new_participant_list, all_series_names, pipeline_ID = \
gather_new_participant_list(output_path_file, output_file_list)
# create the path string for the group analysis output
# replicate the directory path of one of the participant's output
# folder path to the derivative's file, but replace the participant ID
# with the group model name
# this is to ensure nothing gets overwritten between strategies
# or thresholds, etc.
out_dir = os.path.dirname(output_file_list[0]).split(pipeline_ID + '/')
out_dir = out_dir[1].split(out_dir[1].split("/")[-1])[0]
out_dir = os.path.join(group_conf.output_dir, out_dir)
out_dir = out_dir.replace(new_participant_list[0], \
'group_analysis_results_%s/_grp_model_%s' \
% (pipeline_ID, group_conf.model_name))
# !!!!!!!!!!
if (group_conf.repeated_measures == True) and (series_ids[0] != None):
out_dir = out_dir.replace(series_ids[0] + "/", "multiple_series")
# create model file output directories
model_out_dir = os.path.join(group_conf.output_dir, \
'group_analysis_results_%s/_grp_model_%s' \
%(pipeline_ID, group_conf.model_name))
mod_path = os.path.join(model_out_dir, 'model_files')
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
# current_mod_path = folder under
# "/gpa_output/_grp_model_{model name}/model_files/{current derivative}"
current_mod_path = os.path.join(mod_path, resource)
if not os.path.isdir(current_mod_path):
os.makedirs(current_mod_path)
# create new subject list based on which subjects are left after checking
# for missing outputs
new_sub_file = write_new_sub_file(current_mod_path, \
group_conf.subject_list, new_participant_list)
group_conf.update('subject_list', new_sub_file)
# create new design matrix with only the subjects that are left
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
# get the motion statistics parameter file, if present
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
''' okay, here we go... how are we handling series? because here it needs to take in '''
''' the appropriate series to get the appropriate parameter file ! ! ! '''
''' MAY HAVE TO GO BACK ON THIS, and just have one series sent in per this function...'''
power_params_files = {}
measure_list = ['MeanFD_Power', 'MeanFD_Jenkinson', 'MeanDVARS']
for measure in measure_list:
if measure in group_conf.design_formula:
for series_id in all_series_names:
parameter_file = os.path.join(c.outputDirectory, \
pipeline_ID, \
'%s%s_all_params.csv' % \
(series_id.strip('_'), \
threshold_val))
if not os.path.exists(parameter_file):
err = "\n\n[!] CPAC says: Could not find or open the motion "\
"parameter file. This is necessary if you have " \
"included any of the MeanFD measures in your group " \
"model.\n\nThis file can usually be found in the " \
"output directory of your individual-level analysis " \
"runs. If it is not there, double-check to see if " \
"individual-level analysis had completed successfully."\
"\n\nPath not found: %s\n\n" % parameter_file
raise Exception(err)
power_params_files[series_id] = parameter_file
break
else:
power_params_files = None
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, pipeline_ID)
# generate working directory for this output's group analysis run
workDir = '%s/group_analysis/%s/%s' % (c.workingDirectory, \
group_conf.model_name, \
resource)
# this makes strgy_path basically the directory path of the folders after
# the resource/derivative folder level
strgy_path = os.path.dirname(output_file_list[0]).split(resource)[1]
# get rid of periods in the path
for ch in ['.']:
if ch in strgy_path:
strgy_path = strgy_path.replace(ch, "")
# create nipype-workflow-name-friendly strgy_path
# (remove special characters)
strgy_path_name = strgy_path.replace('/', "_")
workDir = workDir + '/' + strgy_path_name
# merge the subjects for this current output
# then, take the group mask, and iterate over the list of subjects
# to extract the mean of each subject using the group mask
merge_output, merge_mask_output, merge_output_dir = \
create_merged_files(workDir, resource, output_file_list)
# CALCULATE THE MEANS of each output using the group mask
derivative_means_dict, roi_means_dict = \
calculate_output_means(resource, output_file_list, \
group_conf.mean_mask, \
group_conf.design_formula, \
group_conf.custom_roi_mask, pipeline_path, \
merge_output_dir, c.identityMatrix)
measure_dict = {}
# extract motion measures from CPAC-generated power params file
if power_params_files != None:
for param_file in power_params_files.values():
new_measure_dict = get_measure_dict(param_file)
measure_dict.update(new_measure_dict)
# combine the motion measures dictionary with the measure_mean
# dictionary (if it exists)
if derivative_means_dict:
measure_dict["Measure_Mean"] = derivative_means_dict
# run create_fsl_model.py to generate the group analysis models
from CPAC.utils import create_fsl_model, kill_me
create_fsl_model.run(group_conf, resource, parameter_file, \
derivative_means_dict, roi_means_dict, \
current_mod_path, True)
# begin GA workflow setup
if not os.path.exists(new_sub_file):
raise Exception("path to input subject list %s is invalid" %
new_sub_file)
#if c.mixedScanAnalysis == True:
# wf = pe.Workflow(name = 'group_analysis/%s/grp_model_%s'%(resource, os.path.basename(model)))
#else:
wf = pe.Workflow(name=resource)
wf.base_dir = workDir
wf.config['execution'] = {
'hash_method': 'timestamp',
'crashdump_dir': os.path.abspath(c.crashLogDirectory)
}
log_dir = os.path.join(group_conf.output_dir, 'logs', 'group_analysis',
resource, 'model_%s' % (group_conf.model_name))
if not os.path.exists(log_dir):
os.makedirs(log_dir)
else:
pass
# gp_flow
# Extracts the model files (.con, .grp, .mat, .fts) from the model
# directory and sends them to the create_group_analysis workflow gpa_wf
gp_flow = create_grp_analysis_dataflow("gp_dataflow_%s" % resource)
gp_flow.inputs.inputspec.grp_model = os.path.join(mod_path, resource)
gp_flow.inputs.inputspec.model_name = group_conf.model_name
gp_flow.inputs.inputspec.ftest = fTest
# gpa_wf
# Creates the actual group analysis workflow
gpa_wf = create_group_analysis(fTest, "gp_analysis_%s" % resource)
gpa_wf.inputs.inputspec.merged_file = merge_output
gpa_wf.inputs.inputspec.merge_mask = merge_mask_output
gpa_wf.inputs.inputspec.z_threshold = z_threshold
gpa_wf.inputs.inputspec.p_threshold = p_threshold
gpa_wf.inputs.inputspec.parameters = (c.FSLDIR, 'MNI152')
wf.connect(gp_flow, 'outputspec.mat', gpa_wf, 'inputspec.mat_file')
wf.connect(gp_flow, 'outputspec.con', gpa_wf, 'inputspec.con_file')
wf.connect(gp_flow, 'outputspec.grp', gpa_wf, 'inputspec.grp_file')
if fTest:
wf.connect(gp_flow, 'outputspec.fts', gpa_wf, 'inputspec.fts_file')
# ds
# Creates the datasink node for group analysis
ds = pe.Node(nio.DataSink(), name='gpa_sink')
if 'sca_roi' in resource:
out_dir = os.path.join(out_dir, \
re.search('sca_roi_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
if 'dr_tempreg_maps_zstat_files_to_standard_smooth' in resource:
out_dir = os.path.join(out_dir, \
re.search('temp_reg_map_z_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
if 'centrality' in resource:
names = ['degree_centrality_binarize', 'degree_centrality_weighted', \
'eigenvector_centrality_binarize', 'eigenvector_centrality_weighted', \
'lfcd_binarize', 'lfcd_weighted']
for name in names:
if name in os.path.basename(output_file_list[0]):
out_dir = os.path.join(out_dir, name)
break
if 'tempreg_maps' in resource:
out_dir = os.path.join(out_dir, \
re.search('\w*[#]*\d+', os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
# if c.mixedScanAnalysis == True:
# out_dir = re.sub(r'(\w)*scan_(\w)*(\d)*(\w)*[/]', '', out_dir)
ds.inputs.base_directory = out_dir
ds.inputs.container = ''
ds.inputs.regexp_substitutions = [(r'(?<=rendered)(.)*[/]', '/'),
(r'(?<=model_files)(.)*[/]', '/'),
(r'(?<=merged)(.)*[/]', '/'),
(r'(?<=stats/clusterMap)(.)*[/]', '/'),
(r'(?<=stats/unthreshold)(.)*[/]', '/'),
(r'(?<=stats/threshold)(.)*[/]', '/'),
(r'_cluster(.)*[/]', ''),
(r'_slicer(.)*[/]', ''),
(r'_overlay(.)*[/]', '')]
########datasink connections#########
if fTest:
wf.connect(gp_flow, 'outputspec.fts', ds, 'model_files.@0')
wf.connect(gp_flow, 'outputspec.mat', ds, 'model_files.@1')
wf.connect(gp_flow, 'outputspec.con', ds, 'model_files.@2')
wf.connect(gp_flow, 'outputspec.grp', ds, 'model_files.@3')
wf.connect(gpa_wf, 'outputspec.merged', ds, 'merged')
wf.connect(gpa_wf, 'outputspec.zstats', ds, 'stats.unthreshold')
wf.connect(gpa_wf, 'outputspec.zfstats', ds, 'stats.unthreshold.@01')
wf.connect(gpa_wf, 'outputspec.fstats', ds, 'stats.unthreshold.@02')
wf.connect(gpa_wf, 'outputspec.cluster_threshold_zf', ds,
'stats.threshold')
wf.connect(gpa_wf, 'outputspec.cluster_index_zf', ds, 'stats.clusterMap')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt_zf', ds,
'stats.clusterMap.@01')
wf.connect(gpa_wf, 'outputspec.overlay_threshold_zf', ds, 'rendered')
wf.connect(gpa_wf, 'outputspec.rendered_image_zf', ds, 'rendered.@01')
wf.connect(gpa_wf, 'outputspec.cluster_threshold', ds,
'stats.threshold.@01')
wf.connect(gpa_wf, 'outputspec.cluster_index', ds, 'stats.clusterMap.@02')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt', ds,
'stats.clusterMap.@03')
wf.connect(gpa_wf, 'outputspec.overlay_threshold', ds, 'rendered.@02')
wf.connect(gpa_wf, 'outputspec.rendered_image', ds, 'rendered.@03')
######################################
# Run the actual group analysis workflow
wf.run()
print "\n\nWorkflow finished for model %s and resource %s\n\n" \
% (os.path.basename(group_conf.output_dir), resource)
def prep_group_analysis_workflow(c, resource, subject_infos):
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
# print "p_id -%s, s_ids -%s, scan_ids -%s, s_paths -%s" %(p_id, s_ids, scan_ids, s_paths)
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path):
# print "phenotypic_file, m_dict", phenotypic_file, m_dict
import csv
reader = csv.reader(open(phenotypic_file, "rU"))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] = []
order[h] = count
count += 1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
if measure in headers:
# check if 'MeanFD is present'
if len(columns[measure]) < 1:
for sub in columns["sub_id"]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(m_dict[sub][measure])
else:
raise Exception("Couldn't find %s value for subject %s" % (measure, sub))
else:
raise Exception("Couldn't find subject %s in the parameter file" % sub)
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exist" % (mod_path)
new_phenotypic_file = os.path.join(mod_path, os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, "w"))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
threshold_val = None
measure_dict = None
measure_list = ["MeanFD", "MeanFD_Jenkinson", "MeanDVARS"]
model_sub_list = []
if re.search("(?<=/_threshold_)\d+.\d+", s_paths[0]):
threshold_val = re.search("(?<=/_threshold_)\d+.\d+", s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print ("Found Multiple threshold value ")
print "threhsold_val -->", threshold_val
if threshold_val:
try:
parameter_file = os.path.join(
c.outputDirectory, p_id[0], "%s_threshold_%s_all_params.csv" % (scan_ids[0].strip("_"), threshold_val)
)
if os.path.exists(parameter_file):
import csv
measure_dict = {}
f = csv.DictReader(open(parameter_file, "r"))
for line in f:
measure_map = {}
for m in measure_list:
if line.get(m):
measure_map[m] = line[m]
measure_dict[line["Subject"]] = measure_map
else:
print "No file name %s found" % parameter_file
except Exception:
print "Exception while extracting parameters from movement file - %s" % (parameter_file)
for config in c.modelConfigs:
import yaml
try:
conf = Configuration(yaml.load(open(os.path.realpath(config), "r")))
except:
raise Exception("Error in reading %s configuration file" % config)
subject_list = [
line.rstrip("\r\n")
for line in open(conf.subjectListFile, "r")
if not (line == "\n") and not line.startswith("#")
]
exist_paths = []
for sub in subject_list:
for path in s_paths:
if sub in path:
exist_paths.append(sub)
if len(list(set(subject_list) - set(exist_paths))) > 0:
print "list of outputs missing for subjects %s for derivative -%s at path- %s" % (
list(set(subject_list) - set(exist_paths)),
resource,
os.path.dirname(s_paths[0]).replace(s_ids[0], "*"),
)
mod_path = os.path.join(
os.path.dirname(s_paths[0]).replace(s_ids[0], "group_analysis_results/_grp_model_%s" % (conf.modelName)),
"model_files",
)
try:
os.makedirs(mod_path)
except:
print "path %s already exists" % mod_path
new_sub_file = os.path.join(mod_path, os.path.basename(conf.subjectListFile))
f = open(new_sub_file, "w")
for sub in exist_paths:
print >> f, sub
f.close()
conf.update("subjectListFile", new_sub_file)
if measure_dict != None:
conf.update(
"phenotypicFile", get_phenotypic_file(conf.phenotypicFile, measure_dict, measure_list, mod_path)
)
print "model config dictionary ->", conf.__dict__
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, True)
except Exception, e:
print "Error in create_fsl_model script"
print e
model_sub_list.append((conf.outputModelFilesDirectory, conf.subjectListFile))
print "model_sub_list ->", model_sub_list
def prep_group_analysis_workflow(c, resource, subject_infos):
#
# this function runs once per output file during group analysis
#
# p_id = a list of pipeline IDs, i.e. the name of the output folder for
# the strat
# s_ids = a list of all the subject IDs
# scan_ids = a list of scan IDs
# s_paths = a list of all of the filepaths of this particular output
# file that prep_group_analysis_workflow is being called for
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] =[]
order[h] = count
count+=1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
print '\n\nMeasure: ', measure, '\n\n'
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
print '\n\ncolumns[sub_id]: ', columns[sub_id], '\n\n'
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(m_dict[sub][measure])
else:
raise Exception("Couldn't find %s value for subject %s"%(measure,sub))
else:
raise Exception("Couldn't find subject %s in the parameter file"%sub)
print '\n\ncolumns[measure]: ', columns, '\n\n'
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exists"%(mod_path)
new_phenotypic_file = os.path.join(mod_path, os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
# END get_phenotypic_file function
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if 1 in c.runScrubbing:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print "Found Multiple threshold value "
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
if len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
import yaml
for config in c.modelConfigs:
print c.modelConfigs
print config
try:
conf = Configuration(yaml.load(open(os.path.realpath(config), 'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
group_sublist = open(conf.subject_list, 'r')
sublist_items = group_sublist.readlines()
subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
print 'subject_list: ', subject_list, '\n\n'
print 's_paths: ', s_paths, '\n\n'
''' begin iteration through group subject list for processing '''
for sub in subject_list:
# let's check to make sure the subject list is formatted for
# repeated measures properly if repeated measures is enabled and
# vice versa
if (c.repeatedMeasures == True) and (',' not in sub):
print '\n\n'
print 'Whoops! The group analysis subject list is not in ' \
'the appropriate format for repeated measures.\n'
print 'Please use the appropriate format as described in ' \
'the CPAC User Guide or turn off Repeated Measures ' \
'in the CPAC pipeline configuration editor, found ' \
'in the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'NOTE: CPAC generates a properly-formatted group ' \
'analysis subject list meant for running repeated ' \
'measures when you create your original subject ' \
'list. Look for \'subject_list_group_analysis_' \
'repeated_measures.txt\' in the directory where ' \
'you created your subject list.\n\n'
raise Exception
elif (c.repeatedMeasures == False) and (',' in sub):
print '\n\n'
print '[!] CPAC says: It looks like your group analysis ' \
'subject list is formatted for running repeated ' \
'measures, but \'Run Repeated Measures\' is not ' \
'enabled in the pipeline configuration, found in ' \
'the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n'
print 'Double-check your pipeline configuration?\n\n'
raise Exception
''' process subject ids for repeated measures, if it is on '''
# if repeated measures is being run and the subject list
# is a list of subject IDs and scan IDs concatenated
if (c.repeatedMeasures == True):
# sub.count(',') equals 1 when there is either multiple scans
# or multiple sessions but not both, for repeated measures
# sub.count(',') equals 2 when there are multiple sessions
# AND scans, for repeated measures
if sub.count(',') == 1:
sub_id = sub.split(',',1)[0]
other_id = sub.split(',',1)[1]
elif sub.count(',') == 2:
sub_id = sub.split(',',2)[0]
scan_id = sub.split(',',2)[1]
session_id = sub.split(',',2)[2]
''' drop subjects from the group subject list '''
# check the path files in path_files_here folder in the subject's
# output folder - and drop any subjects from the group analysis
# subject list which do not exist in the paths to the output files
for path in s_paths:
if (c.repeatedMeasures == True):
if sub.count(',') == 1:
if (sub_id in path) and (other_id in path):
exist_paths.append(sub)
elif sub.count(',') == 2:
if (sub_id in path) and (scan_id in path) and \
(session_id in path):
exist_paths.append(sub)
else:
if sub in path:
exist_paths.append(sub)
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) >0:
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "..for derivatives:"
print resource
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
mod_path = os.path.join(os.path.dirname(s_paths[0]).replace(s_ids[0], 'group_analysis_results/_grp_model_%s'%(conf.model_name)),
'model_files')
print "basename: ", os.path.basename(conf.subject_list)
'''
try:
os.makedirs(mod_path)
print "Creating directory:"
print mod_path
except:
print "Attempted to create directory, but path already exists:"
print mod_path
'''
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
''' write the new subject list '''
new_sub_file = os.path.join(mod_path, os.path.basename(conf.subject_list))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >>f, sub
f.close()
except:
print "Error: Could not open subject list file: ", new_sub_file
raise Exception
conf.update('subjectListFile',new_sub_file)
sub_id = conf.subject_id_label
if measure_dict != None:
conf.update('phenotypicFile',get_phenotypic_file(conf.pheno_file, measure_dict, measure_list, mod_path, sub_id))
print 'conf updated pheno: ', conf.pheno_file, '\n\n'
print "Model config dictionary ->"
print conf.__dict__
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
''' get the motion statistics parameter file, if present '''
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
parameter_file = os.path.join(c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv'%(scan_ids[0].strip('_'),threshold_val))
if 1 in c.runGenerateMotionStatistics:
if not os.path.exists(parameter_file):
print '\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n'
print 'Path not found: ', parameter_file, '\n\n'
raise Exception
elif (1 not in c.runGenerateMotionStatistics) and (os.path.exists(parameter_file)):
if not os.path.exists(parameter_file):
print '\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n'
print 'Path not found: ', parameter_file, '\n\n'
raise Exception
else:
def no_measures_error(measure):
print '\n\n[!] CPAC says: The measure %s was included in ' \
'your group analysis design matrix formula, but ' \
'Generate Motion Statistics was not run during ' \
'individual-level analysis.\n' % measure
print 'Please run Generate Motion Statistics if you wish ' \
'to include this measure in your model.\n'
print 'If you HAVE completed a run with this option ' \
'enabled, then you are seeing this error because ' \
'the motion parameter file normally created by this ' \
'option is missing.\n\n'
raise Exception
for measure in measure_list:
if (measure in conf.design_formula):
no_measures_error(measure)
parameter_file = None
''' run create_fsl_model.py to generate the group analysis models '''
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, p_id[0])
# the current output that cpac_group_analysis_pipeline.py and
# create_fsl_model.py is currently being run for
current_output = s_paths[0].replace(pipeline_path, '').split('/')[2]
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, c.fTest, parameter_file, pipeline_path, current_output, True)
#print >>diag, "> Runs create_fsl_model."
#print >>diag, ""
except Exception, e:
print "FSL Group Analysis model not successfully created - error in create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append((conf.output_dir, conf.subject_list))
def prep_group_analysis_workflow(c, resource, subject_infos):
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
#print "p_id -%s, s_ids -%s, scan_ids -%s, s_paths -%s" %(p_id, s_ids, scan_ids, s_paths)
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
#print "phenotypic_file, m_dict", phenotypic_file, m_dict
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] =[]
order[h] = count
count+=1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(m_dict[sub][measure])
else:
raise Exception("Couldn't find %s value for subject %s"%(measure,sub))
else:
raise Exception("Couldn't find subject %s in the parameter file"%sub)
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exist"%(mod_path)
new_phenotypic_file = os.path.join(mod_path, os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if c.runScrubbing == 1:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print ("Found Multiple threshold value ")
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
print "\n"
#pick the right parameter file from the pipeline folder
#create a dictionary of subject and measures in measure_list
if c.runScrubbing == 1:
try:
parameter_file = os.path.join(c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv'%(scan_ids[0].strip('_'),threshold_val))
if os.path.exists(parameter_file):
import csv
measure_dict = {}
f = csv.DictReader(open(parameter_file,'r'))
for line in f:
measure_map = {}
for m in measure_list:
if line.get(m):
measure_map[m] = line[m]
measure_dict[line['Subject']] = measure_map
else:
print "No file name %s found"%parameter_file
except Exception:
print "Exception while extracting parameters from movement file - %s"%(parameter_file)
for config in c.modelConfigs:
import yaml
try:
conf = Configuration(yaml.load(open(os.path.realpath(config), 'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
subject_list = [line.rstrip('\r\n') for line in open(conf.subjectListFile, 'r') \
if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
# check for missing subject for the derivative
for sub in subject_list :
for path in s_paths:
if sub in path:
exist_paths.append(sub)
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) >0:
print "-------------------------------------------"
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "\n"
print "..for derivatives:"
print resource
print "\n"
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
print "-------------------------------------------"
print '\n'
#import warnings
#warnings.warn(msg)
mod_path = os.path.join(os.path.dirname(s_paths[0]).replace(s_ids[0], 'group_analysis_results/_grp_model_%s'%(conf.modelName)),
'model_files')
print "basename: ", os.path.basename(conf.subjectListFile)
try:
os.makedirs(mod_path)
print "Creating directory:"
print mod_path
print "\n"
except:
print "Attempted to create directory, but path already exists:"
print mod_path
print '\n'
new_sub_file = os.path.join(mod_path, os.path.basename(conf.subjectListFile))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >>f, sub
f.close()
except:
print "Error: Could not open subject list file: ", new_sub_file
print ""
raise Exception
conf.update('subjectListFile',new_sub_file)
sub_id = conf.subjectColumn
if measure_dict != None:
conf.update('phenotypicFile',get_phenotypic_file(conf.phenotypicFile, measure_dict, measure_list, mod_path, sub_id))
print "Model config dictionary ->"
print conf.__dict__
print '\n'
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, True)
except Exception, e:
print "Error in creating models in the create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append((conf.outputModelFilesDirectory, conf.subjectListFile))
print "model_sub_list ->", model_sub_list
def prep_group_analysis_workflow(c, resource, subject_infos):
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
#print "p_id -%s, s_ids -%s, scan_ids -%s, s_paths -%s" %(p_id, s_ids, scan_ids, s_paths)
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
#print "phenotypic_file, m_dict", phenotypic_file, m_dict
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = reader.next()
for h in headers:
columns[h] = []
order[h] = count
count += 1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(
m_dict[sub][measure])
else:
raise Exception(
"Couldn't find %s value for subject %s"
% (measure, sub))
else:
raise Exception(
"Couldn't find subject %s in the parameter file"
% sub)
b = zip(*([k] + columns[k] for k in sorted(columns, key=order.get)))
try:
os.makedirs(mod_path)
except:
print "%s already exist" % (mod_path)
new_phenotypic_file = os.path.join(mod_path,
os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if c.runScrubbing == 1:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+', s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',
s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print("Found Multiple threshold value ")
print "scrubbing threshold_val -->", threshold_val
else:
print "No scrubbing enabled."
print "\n"
#pick the right parameter file from the pipeline folder
#create a dictionary of subject and measures in measure_list
if c.runScrubbing == 1:
try:
parameter_file = os.path.join(
c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv' %
(scan_ids[0].strip('_'), threshold_val))
if os.path.exists(parameter_file):
import csv
measure_dict = {}
f = csv.DictReader(open(parameter_file, 'r'))
for line in f:
measure_map = {}
for m in measure_list:
if line.get(m):
measure_map[m] = line[m]
measure_dict[line['Subject']] = measure_map
else:
print "No file name %s found" % parameter_file
except Exception:
print "Exception while extracting parameters from movement file - %s" % (
parameter_file)
for config in c.modelConfigs:
import yaml
try:
conf = Configuration(yaml.load(open(os.path.realpath(config),
'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
subject_list = [line.rstrip('\r\n') for line in open(conf.subjectListFile, 'r') \
if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
# check for missing subject for the derivative
for sub in subject_list:
for path in s_paths:
if sub in path:
exist_paths.append(sub)
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) > 0:
print "-------------------------------------------"
print "List of outputs missing for subjects:"
print list(set(subject_list) - set(exist_paths))
print "\n"
print "..for derivatives:"
print resource
print "\n"
print "..at paths:"
print os.path.dirname(s_paths[0]).replace(s_ids[0], '*')
print "-------------------------------------------"
print '\n'
#import warnings
#warnings.warn(msg)
mod_path = os.path.join(
os.path.dirname(s_paths[0]).replace(
s_ids[0],
'group_analysis_results/_grp_model_%s' % (conf.modelName)),
'model_files')
print "basename: ", os.path.basename(conf.subjectListFile)
try:
os.makedirs(mod_path)
print "Creating directory:"
print mod_path
print "\n"
except:
print "Attempted to create directory, but path already exists:"
print mod_path
print '\n'
new_sub_file = os.path.join(mod_path,
os.path.basename(conf.subjectListFile))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print >> f, sub
f.close()
except:
print "Error: Could not open subject list file: ", new_sub_file
print ""
raise Exception
conf.update('subjectListFile', new_sub_file)
sub_id = conf.subjectColumn
if measure_dict != None:
conf.update(
'phenotypicFile',
get_phenotypic_file(conf.phenotypicFile, measure_dict,
measure_list, mod_path, sub_id))
print "Model config dictionary ->"
print conf.__dict__
print '\n'
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, True)
except Exception, e:
print "Error in creating models in the create_fsl_model script"
#print "Error ->", e
raise
model_sub_list.append(
(conf.outputModelFilesDirectory, conf.subjectListFile))
print "model_sub_list ->", model_sub_list
def prep_group_analysis_workflow(c, resource, subject_infos):
#
# this function runs once per output file during group analysis
#
# p_id = a list of pipeline IDs, i.e. the name of the output folder for
# the strat
# s_ids = a list of all the subject IDs
# scan_ids = a list of scan IDs
# s_paths = a list of all of the filepaths of this particular output
# file that prep_group_analysis_workflow is being called for
p_id, s_ids, scan_ids, s_paths = (list(tup) for tup in zip(*subject_infos))
# set this to False for now
fTest = False
def get_phenotypic_file(phenotypic_file, m_dict, m_list, mod_path, sub_id):
import csv
reader = csv.reader(open(phenotypic_file, 'rU'))
columns = {}
order = {}
count = 0
headers = next(reader)
for h in headers:
columns[h] =[]
order[h] = count
count+=1
for r in reader:
for h, v in zip(headers, r):
if v:
columns[h].append(str(v))
if m_dict:
for measure in m_list:
print('\n\nMeasure: ', measure, '\n\n')
if measure in headers:
#check if 'MeanFD is present'
if len(columns[measure]) < 1:
print('\n\ncolumns[sub_id]: ', columns[sub_id], '\n\n')
for sub in columns[sub_id]:
if m_dict.get(sub):
if m_dict.get(sub).get(measure):
columns[measure].append(m_dict[sub][measure])
else:
raise Exception("Couldn't find %s value for subject %s"%(measure,sub))
else:
raise Exception("Couldn't find subject %s in the parameter file"%sub)
print('\n\ncolumns[measure]: ', columns, '\n\n')
b = list(zip(*([k] + columns[k] for k in sorted(columns, key=order.get))))
try:
os.makedirs(mod_path)
except:
print("%s already exists"%(mod_path))
new_phenotypic_file = os.path.join(mod_path, os.path.basename(phenotypic_file))
a = csv.writer(open(new_phenotypic_file, 'w'))
for col in b:
a.writerow(list(col))
return new_phenotypic_file
# END get_phenotypic_file function
threshold_val = None
measure_dict = None
measure_list = ['MeanFD', 'MeanFD_Jenkinson', 'MeanDVARS']
model_sub_list = []
if 1 in c.runScrubbing:
#get scrubbing threshold
if re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]):
threshold_val = re.search('(?<=/_threshold_)\d+.\d+',s_paths[0]).group(0)
elif len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
else:
print("Found Multiple threshold value ")
print("scrubbing threshold_val -->", threshold_val)
else:
print("No scrubbing enabled.")
if len(c.scrubbingThreshold) == 1:
threshold_val = c.scrubbingThreshold[0]
import yaml
for config in c.modelConfigs:
print(c.modelConfigs)
print(config)
try:
conf = Configuration(yaml.load(open(os.path.realpath(config), 'r')))
except:
raise Exception("Error in reading %s configuration file" % config)
group_sublist = open(conf.subject_list, 'r')
sublist_items = group_sublist.readlines()
subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
# list of subject paths which DO exist
exist_paths = []
''' begin iteration through group subject list for processing '''
for sub in subject_list:
# let's check to make sure the subject list is formatted for
# repeated measures properly if repeated measures is enabled and
# vice versa
if (c.repeatedMeasures == True) and (',' not in sub):
print('\n\n')
print('[!] CPAC says: The group analysis subject list is ' \
'not inthe appropriate format for repeated ' \
'measures.\n')
print('Please use the appropriate format as described in ' \
'the CPAC User Guide or turn off Repeated Measures ' \
'in the CPAC pipeline configuration editor, found ' \
'in the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n')
print('NOTE: CPAC generates a properly-formatted group ' \
'analysis subject list meant for running repeated ' \
'measures when you create your original subject ' \
'list. Look for \'subject_list_group_analysis_' \
'repeated_measures.txt\' in the directory where ' \
'you created your subject list.\n\n')
raise Exception
elif (c.repeatedMeasures == False) and (',' in sub):
print('\n\n')
print('[!] CPAC says: It looks like your group analysis ' \
'subject list is formatted for running repeated ' \
'measures, but \'Run Repeated Measures\' is not ' \
'enabled in the pipeline configuration, found in ' \
'the \'Group Analysis Settings\' tab of the ' \
'pipeline configuration editor.\n')
print('Double-check your pipeline configuration?\n\n')
raise Exception
''' process subject ids for repeated measures, if it is on '''
# if repeated measures is being run and the subject list
# is a list of subject IDs and scan IDs concatenated
if (c.repeatedMeasures == True):
# sub.count(',') equals 1 when there is either multiple scans
# or multiple sessions but not both, for repeated measures
# sub.count(',') equals 2 when there are multiple sessions
# AND scans, for repeated measures
if sub.count(',') == 1:
sub_id = sub.split(',',1)[0]
other_id = sub.split(',',1)[1]
elif sub.count(',') == 2:
sub_id = sub.split(',',2)[0]
scan_id = sub.split(',',2)[1]
session_id = sub.split(',',2)[2]
''' drop subjects from the group subject list '''
# check the path files in path_files_here folder in the subject's
# output folder - and drop any subjects from the group analysis
# subject list which do not exist in the paths to the output files
for path in s_paths:
if (c.repeatedMeasures == True):
if sub.count(',') == 1:
if (sub_id in path) and (other_id in path):
exist_paths.append(sub)
elif sub.count(',') == 2:
if (sub_id in path) and (scan_id in path) and \
(session_id in path):
exist_paths.append(sub)
else:
if sub in path:
exist_paths.append(sub)
# check to see if any derivatives of subjects are missing
if len(list(set(subject_list) - set(exist_paths))) >0:
print("List of outputs missing for subjects:")
print(list(set(subject_list) - set(exist_paths)))
print("..for derivatives:")
print(resource)
print("..at paths:")
print(os.path.dirname(s_paths[0]).replace(s_ids[0], '*'))
# create the path string for the group analysis output
out_dir = os.path.dirname(s_paths[0]).split(p_id[0] + '/')
out_dir = os.path.join(conf.output_dir, out_dir[1])
out_dir = out_dir.replace(s_ids[0], 'group_analysis_results_%s/_grp_model_%s'%(p_id[0],conf.model_name))
mod_path = os.path.join(out_dir, 'model_files')
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
''' write the new subject list '''
new_sub_file = os.path.join(mod_path, os.path.basename(conf.subject_list))
try:
f = open(new_sub_file, 'w')
for sub in exist_paths:
print(sub, file=f)
f.close()
except:
print("Error: Could not open subject list file: ", new_sub_file)
raise Exception
conf.update('subject_list',new_sub_file)
sub_id = conf.subject_id_label
if measure_dict != None:
conf.update('pheno_file',get_phenotypic_file(conf.pheno_file, measure_dict, measure_list, mod_path, sub_id))
print('conf updated pheno: ', conf.pheno_file, '\n\n')
print("Model config dictionary ->")
print(conf.__dict__)
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
''' get the motion statistics parameter file, if present '''
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
parameter_file = os.path.join(c.outputDirectory, p_id[0], '%s_threshold_%s_all_params.csv'%(scan_ids[0].strip('_'),threshold_val))
if 1 in c.runGenerateMotionStatistics:
if not os.path.exists(parameter_file):
print('\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n')
print('Path not found: ', parameter_file, '\n\n')
raise Exception
elif (1 not in c.runGenerateMotionStatistics) and (os.path.exists(parameter_file)):
if not os.path.exists(parameter_file):
print('\n\n[!] CPAC says: Could not open the parameter file. ' \
'If Generate Motion Statistics is enabled, this can ' \
'usually be found in the output directory of your ' \
'individual-level analysis runs.\n')
print('Path not found: ', parameter_file, '\n\n')
raise Exception
else:
def no_measures_error(measure):
print('\n\n[!] CPAC says: The measure %s was included in ' \
'your group analysis design matrix formula, but ' \
'Generate Motion Statistics was not run during ' \
'individual-level analysis.\n' % measure)
print('Please run Generate Motion Statistics if you wish ' \
'to include this measure in your model.\n')
print('If you HAVE completed a run with this option ' \
'enabled, then you are seeing this error because ' \
'the motion parameter file normally created by this ' \
'option is missing.\n\n')
raise Exception
for measure in measure_list:
if (measure in conf.design_formula):
no_measures_error(measure)
parameter_file = None
''' run create_fsl_model.py to generate the group analysis models '''
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, p_id[0])
# the current output that cpac_group_analysis_pipeline.py and
# create_fsl_model.py is currently being run for
current_output = s_paths[0].replace(pipeline_path, '').split('/')[2]
try:
from CPAC.utils import create_fsl_model
create_fsl_model.run(conf, fTest, parameter_file, pipeline_path, current_output, True)
#print >>diag, "> Runs create_fsl_model."
#print >>diag, ""
except Exception as e:
print("FSL Group Analysis model not successfully created - error in create_fsl_model script")
#print "Error ->", e
raise
model_sub_list.append((conf.output_dir, conf.subject_list))
if len(model_sub_list) == 0:
raise Exception("no model found")
''' start group analysis '''
print('\n\nPreparing the group analysis workflow..\n\n')
for model_sub in model_sub_list:
#print >>diag, "Current model_sub: ", model_sub
#print >>diag, ""
model, subject_list = model_sub
if not os.path.exists(model):
raise Exception("path to model %s doesn't exist"%model)
if not os.path.exists(subject_list):
raise Exception("path to input subject list %s is invalid" % subject_list)
#if c.mixedScanAnalysis == True:
# wf = pe.Workflow(name = 'group_analysis/%s/grp_model_%s'%(resource, os.path.basename(model)))
#else:
# s_paths is a list of paths to each subject's derivative (of the current
# derivative gpa is being run on) - s_paths_dirList is a list of each directory
# in this path separated into list elements
s_paths_dirList = s_paths[0].split('/')
currentDerivativeFile = s_paths_dirList[-1]
currentDerivative = currentDerivativeFile.split('.')[0]
currentDerivative = currentDerivative.replace('#', '_')
strgy_path = os.path.dirname(s_paths[0]).split(scan_ids[0])[1]
for ch in ['.']:
if ch in strgy_path:
strgy_path = strgy_path.replace(ch, '_')
# create nipype-workflow-name-friendly strgy_path
# (remove special characters)
strgy_path_name = strgy_path.replace('/', '__')
wf = pe.Workflow(name = currentDerivative)
workDir = c.workingDirectory + '/group_analysis__%s__grp_model_%s__%s' % (resource, conf.model_name, scan_ids[0])
workDir = workDir + '/' + strgy_path_name
wf.base_dir = workDir
wf.config['execution'] = {'hash_method': 'timestamp', 'crashdump_dir': os.path.abspath(c.crashLogDirectory)}
log_dir = os.path.join(conf.output_dir, 'logs', 'group_analysis', resource, 'model_%s' % (conf.model_name))
if not os.path.exists(log_dir):
os.makedirs(log_dir)
else:
print("log_dir already exist")
# enable logging
from nipype import config
from nipype import logging
config.update_config({'logging': {'log_directory': log_dir,
'log_to_file': True}})
# Temporarily disable until solved
#logging.update_logging(config)
iflogger = logging.getLogger('interface')
''' create the list of paths to all output files to go to model '''
# create the 'ordered_paths' list, which is a list of all of the
# output paths of the output files being included in the current
# group-level analysis model
# 'ordered_paths' is later connected to the 'zmap_files' input
# of the group analysis workflow - the files listed in this list
# are merged into the merged 4D file that goes into group analysis
group_sublist = open(subject_list, 'r')
sublist_items = group_sublist.readlines()
input_subject_list = [line.rstrip('\n') for line in sublist_items \
if not (line == '\n') and not line.startswith('#')]
ordered_paths = []
pathcount = 0
subcount = 0
for sub in input_subject_list:
subcount += 1
if (c.repeatedMeasures == True):
# sub.count(',') equals 1 when there is either multiple scans
# or multiple sessions but not both, for repeated measures
# sub.count(',') equals 2 when there are multiple sessions
# AND scans, for repeated measures
if sub.count(',') == 1:
sub_id = sub.split(',',1)[0]
other_id = sub.split(',',1)[1]
elif sub.count(',') == 2:
sub_id = sub.split(',',2)[0]
scan_id = sub.split(',',2)[1]
session_id = sub.split(',',2)[2]
for path in s_paths:
if (c.repeatedMeasures == True):
# if repeated measures is enabled, make sure all of the
# relevant indicators are in the path before adding it
# to 'ordered_paths', i.e. the session and/or scan IDs
if sub.count(',') == 1:
if (sub_id in path) and (other_id in path):
pathcount += 1
ordered_paths.append(path)
elif sub.count(',') == 2:
if (sub_id in path) and (scan_id in path) and \
(session_id in path):
pathcount += 1
ordered_paths.append(path)
else:
if sub in path:
pathcount += 1
ordered_paths.append(path)
print('S_paths length: ', len(s_paths))
print("Ordered paths length (number of subjects): ", len(ordered_paths))
print("input_subject_list -> %s" % input_subject_list)
print("strgy_path: ", strgy_path)
if len(ordered_paths) == 0:
print('\n\n\n[!] CPAC says: None of the subjects listed in the ' \
'group analysis subject list were found to have outputs ' \
'produced by individual-level analysis.\n\nEnsure that ' \
'the subjects listed in your group analysis subject list ' \
'are the same as the ones included in the individual-' \
'level analysis you are running group-level analysis for.' \
'\n\n\n')
raise Exception
# gp_flow
# Extracts the model files (.con, .grp, .mat, .fts) from the model
# directory and sends them to the create_group_analysis workflow gpa_wf
gp_flow = create_grp_analysis_dataflow("gp_dataflow_%s" % currentDerivative)
gp_flow.inputs.inputspec.grp_model = model
gp_flow.inputs.inputspec.fTest = fTest
# gpa_wf
# Creates the actual group analysis workflow
gpa_wf = create_group_analysis(fTest, "gp_analysis_%s" % currentDerivative)
gpa_wf.inputs.inputspec.zmap_files = ordered_paths
gpa_wf.inputs.inputspec.z_threshold = c.zThreshold
gpa_wf.inputs.inputspec.p_threshold = c.pThreshold
gpa_wf.inputs.inputspec.parameters = (c.FSLDIR, 'MNI152')
print("group model: ", model)
print("f test: ", fTest)
print("z threshold: ", c.zThreshold)
print("p threshold: ", c.pThreshold)
print("parameters: ", (c.FSLDIR, 'MNI152'))
wf.connect(gp_flow, 'outputspec.mat',
gpa_wf, 'inputspec.mat_file')
wf.connect(gp_flow, 'outputspec.con',
gpa_wf, 'inputspec.con_file')
wf.connect(gp_flow, 'outputspec.grp',
gpa_wf, 'inputspec.grp_file')
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
gpa_wf, 'inputspec.fts_file')
# ds
# Creates the datasink node for group analysis
ds = pe.Node(nio.DataSink(), name='gpa_sink')
if 'sca_roi' in resource:
out_dir = os.path.join(out_dir, \
re.search('ROI_number_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(s_paths[0]))[0])[0]).group(0))
if 'centrality' in resource:
names = ['degree_centrality_binarize', 'degree_centrality_weighted', \
'eigenvector_centrality_binarize', 'eigenvector_centrality_weighted', \
'lfcd_binarize', 'lfcd_weighted']
for name in names:
if name in os.path.basename(s_paths[0]):
out_dir = os.path.join(out_dir, name)
break
if 'tempreg_maps_z_files' in resource:
out_dir = os.path.join(out_dir, \
re.search('\w*[#]*\d+', os.path.splitext(os.path.splitext(os.path.basename(s_paths[0]))[0])[0]).group(0))
# if c.mixedScanAnalysis == True:
# out_dir = re.sub(r'(\w)*scan_(\w)*(\d)*(\w)*[/]', '', out_dir)
ds.inputs.base_directory = out_dir
ds.inputs.container = ''
ds.inputs.regexp_substitutions = [(r'(?<=rendered)(.)*[/]','/'),
(r'(?<=model_files)(.)*[/]','/'),
(r'(?<=merged)(.)*[/]','/'),
(r'(?<=stats/clusterMap)(.)*[/]','/'),
(r'(?<=stats/unthreshold)(.)*[/]','/'),
(r'(?<=stats/threshold)(.)*[/]','/'),
(r'_cluster(.)*[/]',''),
(r'_slicer(.)*[/]',''),
(r'_overlay(.)*[/]','')]
'''
if 1 in c.runSymbolicLinks:
link_node = pe.MapNode(interface=util.Function(
input_names=['in_file',
'resource'],
output_names=[],
function=prepare_gp_links),
name='link_gp_', iterfield=['in_file'])
link_node.inputs.resource = resource
wf.connect(ds, 'out_file', link_node, 'in_file')
'''
########datasink connections#########
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
ds, 'model_files.@0')
wf.connect(gp_flow, 'outputspec.mat',
ds, 'model_files.@1' )
wf.connect(gp_flow, 'outputspec.con',
ds, 'model_files.@2')
wf.connect(gp_flow, 'outputspec.grp',
ds, 'model_files.@3')
wf.connect(gpa_wf, 'outputspec.merged',
ds, 'merged')
wf.connect(gpa_wf, 'outputspec.zstats',
ds, 'stats.unthreshold')
wf.connect(gpa_wf, 'outputspec.zfstats',
ds,'stats.unthreshold.@01')
wf.connect(gpa_wf, 'outputspec.fstats',
ds,'stats.unthreshold.@02')
wf.connect(gpa_wf, 'outputspec.cluster_threshold_zf',
ds, 'stats.threshold')
wf.connect(gpa_wf, 'outputspec.cluster_index_zf',
ds,'stats.clusterMap')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt_zf',
ds, 'stats.clusterMap.@01')
wf.connect(gpa_wf, 'outputspec.overlay_threshold_zf',
ds, 'rendered')
wf.connect(gpa_wf, 'outputspec.rendered_image_zf',
ds, 'rendered.@01')
wf.connect(gpa_wf, 'outputspec.cluster_threshold',
ds, 'stats.threshold.@01')
wf.connect(gpa_wf, 'outputspec.cluster_index',
ds, 'stats.clusterMap.@02')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt',
ds, 'stats.clusterMap.@03')
wf.connect(gpa_wf, 'outputspec.overlay_threshold',
ds, 'rendered.@02')
wf.connect(gpa_wf, 'outputspec.rendered_image',
ds, 'rendered.@03')
######################################
# Run the actual group analysis workflow
wf.run()
'''
except:
print "Error: Group analysis workflow run command did not complete successfully."
print "subcount: ", subcount
print "pathcount: ", pathcount
print "sublist: ", sublist_items
print "input subject list: "
print "conf: ", conf.subjectListFile
raise Exception
'''
print("**Workflow finished for model %s and resource %s"%(os.path.basename(model), resource))
def prep_group_analysis_workflow(model_df, pipeline_config_obj, \
model_name, group_config_obj, resource_id, preproc_strat, \
series_or_repeated_label):
#
# this function runs once per derivative type and preproc strat combo
# during group analysis
#
import os
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
pipeline_ID = pipeline_config_obj.pipeline_name
# get thresholds
z_threshold = float(group_config_obj.z_threshold[0])
p_threshold = float(group_config_obj.p_threshold[0])
sub_id_label = group_config_obj.subject_id_label
# determine if f-tests are included or not
custom_confile = group_config_obj.custom_contrasts
if ((custom_confile == None) or (custom_confile == '') or \
("None" in custom_confile) or ("none" in custom_confile)):
if (len(group_config_obj.f_tests) == 0) or \
(group_config_obj.f_tests == None):
fTest = False
else:
fTest = True
else:
if not os.path.exists(custom_confile):
errmsg = "\n[!] CPAC says: You've specified a custom contrasts " \
".CSV file for your group model, but this file cannot " \
"be found. Please double-check the filepath you have " \
"entered.\n\nFilepath: %s\n\n" % custom_confile
raise Exception(errmsg)
with open(custom_confile,"r") as f:
evs = f.readline()
evs = evs.rstrip('\r\n').split(',')
count_ftests = 0
fTest = False
for ev in evs:
if "f_test" in ev:
count_ftests += 1
if count_ftests > 0:
fTest = True
# create path for output directory
out_dir = os.path.join(group_config_obj.output_dir, \
"group_analysis_results_%s" % pipeline_ID, \
"group_model_%s" % model_name, resource_id, \
series_or_repeated_label, preproc_strat)
model_path = os.path.join(out_dir, 'model_files')
# generate working directory for this output's group analysis run
work_dir = os.path.join(c.workingDirectory, "group_analysis", model_name,\
resource_id, series_or_repeated_label, preproc_strat)
log_dir = os.path.join(out_dir, 'logs', resource_id, \
'model_%s' % model_name)
# create the actual directories
if not os.path.isdir(model_path):
try:
os.makedirs(model_path)
except Exception as e:
err = "\n\n[!] Could not create the group analysis output " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
if not os.path.isdir(work_dir):
try:
os.makedirs(work_dir)
except Exception as e:
err = "\n\n[!] Could not create the group analysis working " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
if not os.path.isdir(log_dir):
try:
os.makedirs(log_dir)
except Exception as e:
err = "\n\n[!] Could not create the group analysis logfile " \
"directories.\n\nAttempted directory creation: %s\n\n" \
"Error details: %s\n\n" % (model_path, e)
raise Exception(err)
# create new subject list based on which subjects are left after checking
# for missing outputs
new_participant_list = []
for part in list(model_df["Participant"]):
# do this instead of using "set" just in case, to preserve order
# only reason there may be duplicates is because of multiple-series
# repeated measures runs
if part not in new_participant_list:
new_participant_list.append(part)
new_sub_file = write_new_sub_file(model_path, \
group_config_obj.participant_list, \
new_participant_list)
group_conf.update('participant_list',new_sub_file)
# start processing the dataframe further
design_formula = group_config_obj.design_formula
# demean the motion params
if ("MeanFD" in design_formula) or ("MeanDVARS" in design_formula):
params = ["MeanFD_Power", "MeanFD_Jenkinson", "MeanDVARS"]
for param in params:
model_df[param] = model_df[param].astype(float)
model_df[param] = model_df[param].sub(model_df[param].mean())
# create 4D merged copefile, in the correct order, identical to design
# matrix
merge_outfile = model_name + "_" + resource_id + "_merged.nii.gz"
merge_outfile = os.path.join(model_path, merge_outfile)
merge_file = create_merged_copefile(list(model_df["Filepath"]), \
merge_outfile)
# create merged group mask
if group_config_obj.mean_mask[0] == "Group Mask":
merge_mask_outfile = os.path.basename(merge_file) + "_mask.nii.gz"
merge_mask = create_merged_mask(merge_file, merge_mask_outfile)
# calculate measure means, and demean
if "Measure_Mean" in design_formula:
model_df = calculate_measure_mean_in_df(model_df, merge_mask)
# calculate custom ROIs, and demean (in workflow?)
if "Custom_ROI_Mean" in design_formula:
custom_roi_mask = group_config_obj.custom_roi_mask
if (custom_roi_mask == None) or (custom_roi_mask == "None") or \
(custom_roi_mask == "none") or (custom_roi_mask == ""):
err = "\n\n[!] You included 'Custom_ROI_Mean' in your design " \
"formula, but you didn't supply a custom ROI mask file." \
"\n\nDesign formula: %s\n\n" % design_formula
raise Exception(err)
# make sure the custom ROI mask file is the same resolution as the
# output files - if not, resample and warn the user
roi_mask = check_mask_file_resolution(list(model_df["Raw_Filepath"])[0], \
custom_roi_mask, model_path, \
resource_id)
# if using group merged mask, trim the custom ROI mask to be within
# its constraints
if merge_mask:
output_mask = os.path.join(model_path, "group_masked_%s" \
% os.path.basename(input_mask))
roi_mask = trim_mask(roi_mask, merge_mask, output_mask)
# calculate
model_df = calculate_custom_roi_mean_in_df(model_df, roi_mask)
# modeling group variances separately
# add repeated measures 1's matrices
# patsify model DF, drop columns not in design formula
# process contrasts
wf = pe.Workflow(name=resource_id)
wf.base_dir = work_dir
crash_dir = os.path.join(pipeline_config_obj.crashLogDirectory, \
"group_analysis", model_name)
wf.config['execution'] = {'hash_method': 'timestamp', \
'crashdump_dir': crash_dir}
if "Measure_Mean" in design_formula:
measure_mean = pe.Node(util.Function(input_names=['model_df',
'merge_mask'],
output_names=['model_df'],
function=calculate_measure_mean_in_df),
name='measure_mean')
measure_mean.inputs.model_df = model_df
wf.connect(merge_mask, "out_file", measure_mean, "merge_mask")
if "Custom_ROI_Mean" in design_formula:
roi_mean = pe.Node(util.Function())
group_config_obj.custom_roi_mask
#----------------
import yaml
import pandas as pd
# load group analysis model configuration file
try:
with open(os.path.realpath(group_config_file),"r") as f:
group_conf = Configuration(yaml.load(f))
except Exception as e:
err_string = "\n\n[!] CPAC says: Could not read group model " \
"configuration YML file. Ensure you have read access " \
"for the file and that it is formatted properly.\n\n" \
"Configuration file: %s\n\nError details: %s" \
% (group_config_file, e)
raise Exception(err_string)
# gather all of the information
# - lists of all the participant unique IDs (participant_site_session) and
# of all of the series IDs present in output_file_list
# - also returns the pipeline ID
new_participant_list, all_series_names, pipeline_ID = \
gather_new_participant_list(output_path_file, output_file_list)
# create the path string for the group analysis output
# replicate the directory path of one of the participant's output
# folder path to the derivative's file, but replace the participant ID
# with the group model name
# this is to ensure nothing gets overwritten between strategies
# or thresholds, etc.
out_dir = os.path.dirname(output_file_list[0]).split(pipeline_ID + '/')
out_dir = out_dir[1].split(out_dir[1].split("/")[-1])[0]
out_dir = os.path.join(group_conf.output_dir, out_dir)
out_dir = out_dir.replace(new_participant_list[0], \
'group_analysis_results_%s/_grp_model_%s' \
% (pipeline_ID, group_conf.model_name))
# !!!!!!!!!!
if (group_conf.repeated_measures == True) and (series_ids[0] != None):
out_dir = out_dir.replace(series_ids[0] + "/", "multiple_series")
# create model file output directories
model_out_dir = os.path.join(group_conf.output_dir, \
'group_analysis_results_%s/_grp_model_%s' \
%(pipeline_ID, group_conf.model_name))
mod_path = os.path.join(model_out_dir, 'model_files')
if not os.path.isdir(mod_path):
os.makedirs(mod_path)
# current_mod_path = folder under
# "/gpa_output/_grp_model_{model name}/model_files/{current derivative}"
current_mod_path = os.path.join(mod_path, resource)
if not os.path.isdir(current_mod_path):
os.makedirs(current_mod_path)
# create new subject list based on which subjects are left after checking
# for missing outputs
new_sub_file = write_new_sub_file(current_mod_path, \
group_conf.subject_list, new_participant_list)
group_conf.update('subject_list',new_sub_file)
# create new design matrix with only the subjects that are left
# Run 'create_fsl_model' script to extract phenotypic data from
# the phenotypic file for each of the subjects in the subject list
# get the motion statistics parameter file, if present
# get the parameter file so it can be passed to create_fsl_model.py
# so MeanFD or other measures can be included in the design matrix
''' okay, here we go... how are we handling series? because here it needs to take in '''
''' the appropriate series to get the appropriate parameter file ! ! ! '''
''' MAY HAVE TO GO BACK ON THIS, and just have one series sent in per this function...'''
power_params_files = {}
measure_list = ['MeanFD_Power', 'MeanFD_Jenkinson', 'MeanDVARS']
for measure in measure_list:
if measure in group_conf.design_formula:
for series_id in all_series_names:
parameter_file = os.path.join(c.outputDirectory, \
pipeline_ID, \
'%s%s_all_params.csv' % \
(series_id.strip('_'), \
threshold_val))
if not os.path.exists(parameter_file):
err = "\n\n[!] CPAC says: Could not find or open the motion "\
"parameter file. This is necessary if you have " \
"included any of the MeanFD measures in your group " \
"model.\n\nThis file can usually be found in the " \
"output directory of your individual-level analysis " \
"runs. If it is not there, double-check to see if " \
"individual-level analysis had completed successfully."\
"\n\nPath not found: %s\n\n" % parameter_file
raise Exception(err)
power_params_files[series_id] = parameter_file
break
else:
power_params_files = None
# path to the pipeline folder to be passed to create_fsl_model.py
# so that certain files like output_means.csv can be accessed
pipeline_path = os.path.join(c.outputDirectory, pipeline_ID)
# generate working directory for this output's group analysis run
workDir = '%s/group_analysis/%s/%s' % (c.workingDirectory, \
group_conf.model_name, \
resource)
# this makes strgy_path basically the directory path of the folders after
# the resource/derivative folder level
strgy_path = os.path.dirname(output_file_list[0]).split(resource)[1]
# get rid of periods in the path
for ch in ['.']:
if ch in strgy_path:
strgy_path = strgy_path.replace(ch, "")
# create nipype-workflow-name-friendly strgy_path
# (remove special characters)
strgy_path_name = strgy_path.replace('/', "_")
workDir = workDir + '/' + strgy_path_name
# merge the subjects for this current output
# then, take the group mask, and iterate over the list of subjects
# to extract the mean of each subject using the group mask
merge_output, merge_mask_output, merge_output_dir = \
create_merged_files(workDir, resource, output_file_list)
# CALCULATE THE MEANS of each output using the group mask
derivative_means_dict, roi_means_dict = \
calculate_output_means(resource, output_file_list, \
group_conf.mean_mask, \
group_conf.design_formula, \
group_conf.custom_roi_mask, pipeline_path, \
merge_output_dir, c.identityMatrix)
measure_dict = {}
# extract motion measures from CPAC-generated power params file
if power_params_files != None:
for param_file in power_params_files.values():
new_measure_dict = get_measure_dict(param_file)
measure_dict.update(new_measure_dict)
# combine the motion measures dictionary with the measure_mean
# dictionary (if it exists)
if derivative_means_dict:
measure_dict["Measure_Mean"] = derivative_means_dict
# run create_fsl_model.py to generate the group analysis models
from CPAC.utils import create_fsl_model, kill_me
create_fsl_model.run(group_conf, resource, parameter_file, \
derivative_means_dict, roi_means_dict, \
current_mod_path, True)
# begin GA workflow setup
if not os.path.exists(new_sub_file):
raise Exception("path to input subject list %s is invalid" % new_sub_file)
#if c.mixedScanAnalysis == True:
# wf = pe.Workflow(name = 'group_analysis/%s/grp_model_%s'%(resource, os.path.basename(model)))
#else:
wf = pe.Workflow(name = resource)
wf.base_dir = workDir
wf.config['execution'] = {'hash_method': 'timestamp', 'crashdump_dir': os.path.abspath(c.crashLogDirectory)}
log_dir = os.path.join(group_conf.output_dir, 'logs', 'group_analysis', resource, 'model_%s' % (group_conf.model_name))
if not os.path.exists(log_dir):
os.makedirs(log_dir)
else:
pass
# gp_flow
# Extracts the model files (.con, .grp, .mat, .fts) from the model
# directory and sends them to the create_group_analysis workflow gpa_wf
gp_flow = create_grp_analysis_dataflow("gp_dataflow_%s" % resource)
gp_flow.inputs.inputspec.grp_model = os.path.join(mod_path, resource)
gp_flow.inputs.inputspec.model_name = group_conf.model_name
gp_flow.inputs.inputspec.ftest = fTest
# gpa_wf
# Creates the actual group analysis workflow
gpa_wf = create_group_analysis(fTest, "gp_analysis_%s" % resource)
gpa_wf.inputs.inputspec.merged_file = merge_output
gpa_wf.inputs.inputspec.merge_mask = merge_mask_output
gpa_wf.inputs.inputspec.z_threshold = z_threshold
gpa_wf.inputs.inputspec.p_threshold = p_threshold
gpa_wf.inputs.inputspec.parameters = (c.FSLDIR, 'MNI152')
wf.connect(gp_flow, 'outputspec.mat',
gpa_wf, 'inputspec.mat_file')
wf.connect(gp_flow, 'outputspec.con',
gpa_wf, 'inputspec.con_file')
wf.connect(gp_flow, 'outputspec.grp',
gpa_wf, 'inputspec.grp_file')
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
gpa_wf, 'inputspec.fts_file')
# ds
# Creates the datasink node for group analysis
ds = pe.Node(nio.DataSink(), name='gpa_sink')
if 'sca_roi' in resource:
out_dir = os.path.join(out_dir, \
re.search('sca_roi_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
if 'dr_tempreg_maps_zstat_files_to_standard_smooth' in resource:
out_dir = os.path.join(out_dir, \
re.search('temp_reg_map_z_(\d)+',os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
if 'centrality' in resource:
names = ['degree_centrality_binarize', 'degree_centrality_weighted', \
'eigenvector_centrality_binarize', 'eigenvector_centrality_weighted', \
'lfcd_binarize', 'lfcd_weighted']
for name in names:
if name in os.path.basename(output_file_list[0]):
out_dir = os.path.join(out_dir, name)
break
if 'tempreg_maps' in resource:
out_dir = os.path.join(out_dir, \
re.search('\w*[#]*\d+', os.path.splitext(os.path.splitext(os.path.basename(output_file_list[0]))[0])[0]).group(0))
# if c.mixedScanAnalysis == True:
# out_dir = re.sub(r'(\w)*scan_(\w)*(\d)*(\w)*[/]', '', out_dir)
ds.inputs.base_directory = out_dir
ds.inputs.container = ''
ds.inputs.regexp_substitutions = [(r'(?<=rendered)(.)*[/]','/'),
(r'(?<=model_files)(.)*[/]','/'),
(r'(?<=merged)(.)*[/]','/'),
(r'(?<=stats/clusterMap)(.)*[/]','/'),
(r'(?<=stats/unthreshold)(.)*[/]','/'),
(r'(?<=stats/threshold)(.)*[/]','/'),
(r'_cluster(.)*[/]',''),
(r'_slicer(.)*[/]',''),
(r'_overlay(.)*[/]','')]
########datasink connections#########
if fTest:
wf.connect(gp_flow, 'outputspec.fts',
ds, 'model_files.@0')
wf.connect(gp_flow, 'outputspec.mat',
ds, 'model_files.@1' )
wf.connect(gp_flow, 'outputspec.con',
ds, 'model_files.@2')
wf.connect(gp_flow, 'outputspec.grp',
ds, 'model_files.@3')
wf.connect(gpa_wf, 'outputspec.merged',
ds, 'merged')
wf.connect(gpa_wf, 'outputspec.zstats',
ds, 'stats.unthreshold')
wf.connect(gpa_wf, 'outputspec.zfstats',
ds,'stats.unthreshold.@01')
wf.connect(gpa_wf, 'outputspec.fstats',
ds,'stats.unthreshold.@02')
wf.connect(gpa_wf, 'outputspec.cluster_threshold_zf',
ds, 'stats.threshold')
wf.connect(gpa_wf, 'outputspec.cluster_index_zf',
ds,'stats.clusterMap')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt_zf',
ds, 'stats.clusterMap.@01')
wf.connect(gpa_wf, 'outputspec.overlay_threshold_zf',
ds, 'rendered')
wf.connect(gpa_wf, 'outputspec.rendered_image_zf',
ds, 'rendered.@01')
wf.connect(gpa_wf, 'outputspec.cluster_threshold',
ds, 'stats.threshold.@01')
wf.connect(gpa_wf, 'outputspec.cluster_index',
ds, 'stats.clusterMap.@02')
wf.connect(gpa_wf, 'outputspec.cluster_localmax_txt',
ds, 'stats.clusterMap.@03')
wf.connect(gpa_wf, 'outputspec.overlay_threshold',
ds, 'rendered.@02')
wf.connect(gpa_wf, 'outputspec.rendered_image',
ds, 'rendered.@03')
######################################
# Run the actual group analysis workflow
wf.run()
print "\n\nWorkflow finished for model %s and resource %s\n\n" \
% (os.path.basename(group_conf.output_dir), resource)