def extractFSasegstats(directory, outfile):
'''Generate a command-line command to extract freesurfer
Parameters
----------
directory : string
Full path to root directory of freesurfer processed data. Expect file tree
to be directory/sub/stats/aseg.stats
outfile : string
Full path to directory where summary file should be saved
Returns
-------
subs : list
List of subjects found in the input directory
commandlinestr : string
String that was passed to the command line
output : string
Command line output
'''
subs, _ = cf.lbls_infold(directory)
subs = [sub for sub in subs if 'long' not in sub]
subpaths = ['%s%s/stats/aseg.stats' % (directory, sub) for sub in subs]
sublist = ' '.join(subpaths)
commandlinestr = 'asegstats2table --inputs %s --skip --tablefile %s' % (sublist, outfile)
process = subprocess.Popen(commandlinestr.split(), stdout=subprocess.PIPE)
output = process.communicate()[0]
return subs, commandlinestr, output
def bacs_pet_mri_date_batch(rootpath):
"""Given a path, this function finds subject folders there and finds
the date of the freesurfer processed data.
Parameters
----------
rootpath : string
Path where subject directories lie
Returns
-------
datetbl : DataFrame
Holds codea, MRI_Tp, and MRI_Scandate fields
"""
subs, _ = cf.lbls_infold(rootpath)
datetbl = pd.DataFrame(columns=['sub'], data=subs)
datetbl['MRI_Scandate'] = float('NaN')
for sub in subs:
dateout = bacs_pet_mri_date(rootpath, sub)
datetbl.loc[datetbl['sub']==sub,'MRI_Scandate'] = dateout
datetbl['codea'] = [cf.get_lbl_id(sub) for sub in datetbl['sub'].tolist()]
datetbl['MRI_Tp'] = [cf.get_tp(sub) for sub in datetbl['sub'].tolist()]
datetbl.drop('sub', axis=1, inplace=True)
datetbl = datetbl[datetbl['MRI_Tp'].notnull()]
return datetbl