(tpath, se) = cmd_stdout("which mri_info")

assert(len(se) == 0)

if len(tpath) == 0:

raise Exception, "Unable to find the required program: mri_info"

(so, se) = cmd_stdout("mri_info %s" % dfn)

assert(len(se) == 0)

so = so.split("\n")

nVols = -1

for (i1, tline) in enumerate(so):

if len(tline) == 0:

continue

tline = tline.strip()

if tline.startswith("dimensions"):

nVols = int(tline.split(" ")[-1])

break

# From Satrajit Ghosh's code at: https://github.com/satra/nipype/blob/enh/restingwf/examples/rsfmri_preprocessing.py#L47

from dcmstack.extract import default_extractor

from dicom import read_file

from nipype.utils.filemanip import filename_to_list

meta = default_extractor(read_file(filename_to_list(dicom_files)[0],

stop_before_pixels=True,

force=True))

return (meta['RepetitionTime'] / 1000., meta['CsaImage.MosaicRefAcqTimes'],

check_file(inImg, logFN=logFN)

check_file(refImg, logFN=logFN)

check_file(xfmMat, logFN=logFN)

cmd = "flirt -in %s -ref %s -applyxfm -init %s -out %s " % \

(inImg, refImg, xfmMat, outImg)

if interpMeth != "":

cmd += "-interp %s " % interpMeth

saydo(cmd, logFN=logFN)

check_bin_path("convert_xfm", logFN=logFN)

check_file(inMatFN, logFN=logFN)

cvtCmd = "convert_xfm -omat %s -inverse %s " % (outMatFN, inMatFN)

saydo(cvtCmd, logFN=logFN)

ctabf = open(ctabfn, 'r')

ctxt = ctabf.read().split('\n')

ctabf.close()

roi_nums = []

roi_names = []

for clin in ctxt:

clin = clin.replace("\t", " ")

if len(clin) == 0:

continue

clin = clin.split(' ')

while clin.count('') > 0:

clin.remove('')

#print(clin) # DEBUG

if clin[1] == 'unknown' or clin[1] == 'bankssts' \

or clin[1] == "corpuscallosum" or clin[1] == "Unknown" \

or clin[1].startswith("None"):

continue

roi_nums.append(int(clin[0]))

roi_names.append(clin[1])

check_file(imgFN)

check_bin_path("fslstats")

(so, se) = cmd_stdout("fslstats %s -V" % imgFN)

assert(len(se) == 0)

so = so.split(" ")

assert(len(so) >= 2)

nVoxels = int(so[0])

mm3 = float(so[1])