def test_mlab_init():
yield assert_equal, mlab.MatlabCommand._cmd, 'matlab'
yield assert_equal, mlab.MatlabCommand.input_spec, mlab.MatlabInputSpec
yield assert_equal, mlab.MatlabCommand().cmd, matlab_cmd
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_equal, mc.cmd, 'foo_m'
def test_run_interface():
default_script_file = clean_workspace_and_get_default_script_file()
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 1.'
yield assert_raises, ValueError, mc.run # script is mandatory
yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 2.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
mc.inputs.script = 'a=1;'
yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 3.'
yield assert_raises, IOError, mc.run # foo_m is not an executable
yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 3.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
cwd = os.getcwd()
basedir = mkdtemp()
os.chdir(basedir)
# bypasses ubuntu dash issue
mc = mlab.MatlabCommand(script='foo;', paths=[basedir], mfile=True)
yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 4.'
yield assert_raises, RuntimeError, mc.run
yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 4.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
# bypasses ubuntu dash issue
res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run()
yield assert_equal, res.runtime.returncode, 0
yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 5.'
os.chdir(cwd)
rmtree(basedir)
def test_mlab_init():
default_script_file = clean_workspace_and_get_default_script_file()
yield assert_equal, mlab.MatlabCommand._cmd, 'matlab'
yield assert_equal, mlab.MatlabCommand.input_spec, mlab.MatlabInputSpec
yield assert_equal, mlab.MatlabCommand().cmd, matlab_cmd
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_equal, mc.cmd, 'foo_m'
def test_mlab_init():
default_script_file = clean_workspace_and_get_default_script_file()
assert mlab.MatlabCommand._cmd == 'matlab'
assert mlab.MatlabCommand.input_spec == mlab.MatlabInputSpec
assert mlab.MatlabCommand().cmd == matlab_cmd
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
assert mc.cmd == 'foo_m'
def runCSbyMatlab(inputScan, inputMask, CSScanFileName,
Path_to_Matlab_Func):
"""
This Function takes in...
:param inputScan:
:param inputMask:
:param CSScanFileName:
:param Path_to_Matlab_Func:
:return: outputCSFilename
"""
import os
import nipype.interfaces.matlab as matlab
script = "runCS('" + inputScan + "','" + inputMask + "','" + CSScanFileName + "')"
mlab = matlab.MatlabCommand()
mlab.set_default_matlab_cmd("matlab")
mlab.inputs.single_comp_thread = False
mlab.inputs.nodesktop = True
mlab.inputs.nosplash = True
mlab.inputs.paths = Path_to_Matlab_Func
mlab.inputs.script = script
mlab.run()
outputCSFilename = os.path.join(
os.getcwd(), CSScanFileName) # return output CS filename
assert os.path.isfile(
outputCSFilename), "CS file is not found: %s" % outputCSFilename
return outputCSFilename
def spm_matrix(params):
"""Run the spm function spm_matrix through Matlab.
Parameters
==========
params : 1D numpy.ndarray, shape > 6
Parameters to convert to the affine transfomation matrix.
Returns
=======
affine : numpy.ndarray of shape (4, 4)
The affine transformation matrix.
"""
# TODO write using _make_matlab_command to rely only on SPM
params_str = '[{0}, {1}, {2}, {3}, {4}, {5}]'.format(*params)
mat_path = '/tmp/matrix.mat'
# Generate the Matlab script
mlab = matlab.MatlabCommand()
mlab.inputs.script = "\naddpath '/i2bm/local/spm8-6313/' \n" + \
"matrix = spm_matrix(" + params_str + ");\n" + \
"save('" + mat_path + "', 'matrix')"
# Run the script and load the output matrix
mlab.run()
mat_dict = loadmat(mat_path)
affine = mat_dict['matrix']
return affine
def test_run_interface():
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_raises, ValueError, mc.run # script is mandatory
mc.inputs.script = 'a=1;'
yield assert_raises, IOError, mc.run # foo_m is not an executable
cwd = os.getcwd()
basedir = mkdtemp()
os.chdir(basedir)
# bypasses ubuntu dash issue
mc = mlab.MatlabCommand(script='foo;', paths=[basedir], mfile=True)
yield assert_raises, RuntimeError, mc.run
# bypasses ubuntu dash issue
res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run()
yield assert_equal, res.runtime.returncode, 0
os.chdir(cwd)
rmtree(basedir)
def reslice(space_define, infile):
""" uses spm_reslice to resample infile into the space
of space_define, assumes they are already in register"""
startdir = os.getcwd()
pth, _ = os.path.split(infile)
os.chdir(pth)
mlab_cmd = mlab.MatlabCommand(matlab_cmd='matlab-spm8')
mlab_cmd.inputs.nodesktop = True
mlab_cmd.inputs.nosplash = True
mlab_cmd.inputs.mfile = True
mlab_cmd.inputs.ignore_exception = True
mlab_cmd.inputs.script_file = 'pyspm8_reslice.m'
script = """
flags.mean = 0;
flags.which = 1;
flags.mask = 1;
flags.interp = 0;
infiles = strvcat(\'%s\', \'%s\');
invols = spm_vol(infiles);
spm_reslice(invols, flags);
""" % (space_define, infile)
mlab_cmd.inputs.script = script
mout = mlab_cmd.run()
os.chdir(startdir)
return mout
def __init__(self, script='', **options):
import nipype.interfaces.matlab as matlab
mlab = matlab.MatlabCommand(mfile=False)
mlab.inputs.script = script
for ef in options:
setattr(mlab.inputs, ef, options[ef])
self.res = mlab.run()
def spm_imatrix(affine):
"""Run the spm function spm_imatrix through Matlab.
Parameters
==========
affine : numpy.ndarray of shape (4, 4)
The affine transformation matrix.
Returns
=======
params : 1D numpy.ndarray
The parameters of the affine transformation.
"""
affine_str = "["
for row in affine:
affine_str += '{0}, {1}, {2}, {3};'.format(*row)
affine_str = affine_str[:-1]
affine_str += "]"
# Generate the Matlab script
mat_path = '/tmp/params.mat'
mlab = matlab.MatlabCommand()
mlab.inputs.script = "\naddpath '/i2bm/local/spm8-6313/' \n" +\
"parameters = spm_imatrix(" + affine_str + ");\n" +\
"save('" + mat_path + "', 'parameters')"
# Run the script and load the output vector
mlab.run()
mat_dict = loadmat(mat_path)
params = mat_dict['parameters']
params = np.squeeze(params)
return params
def forward_coreg(mri, pet, transform):
""" coregisters pet to mri and applies to pet,
saves parameters in transform """
startdir = os.getcwd()
pth, _ = os.path.split(pet)
os.chdir(pth)
mlab_cmd = mlab.MatlabCommand(matlab_cmd='matlab-spm8')
mlab_cmd.inputs.nodesktop = True
mlab_cmd.inputs.nosplash = True
mlab_cmd.inputs.mfile = True
mlab_cmd.inputs.script_file = 'pyspm8_invert_coreg.m'
script = """
pet = \'%s\';
mri = \'%s\';
petv = spm_vol(pet);
mriv = spm_vol(mri);
x = spm_coreg(petv, mriv);
M = spm_matrix(x(:)');
save( \'%s\' , \'M\' );
petspace = spm_get_space(pet);
spm_get_space(pet, M * petspace);
""" % (pet, mri, transform)
mlab_cmd.inputs.script = script
mout = mlab_cmd.run()
os.chdir(startdir)
return mout
def test_set_matlabcmd():
default_script_file = clean_workspace_and_get_default_script_file()
mi = mlab.MatlabCommand()
mi.set_default_matlab_cmd('foo')
yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist.'
yield assert_equal, mi._default_matlab_cmd, 'foo'
mi.set_default_matlab_cmd(matlab_cmd)
def test_set_matlabcmd():
default_script_file = clean_workspace_and_get_default_script_file()
mi = mlab.MatlabCommand()
mi.set_default_matlab_cmd('foo')
assert not os.path.exists(
default_script_file), 'scriptfile should not exist.'
assert mi._default_matlab_cmd == 'foo'
mi.set_default_matlab_cmd(matlab_cmd)
def CBFscale_PWI_data(all_aligned_dir):
# Envoke matlab to calculate scaled-CBF from PWI data
mlc = mlab.MatlabCommand()
cmd = "cd('%s');raw_pwi = spm_vol('diffdata_mean.nii');scaled_pwi = raw_pwi;scaled_pwi.fname = 'CBF_Scaled_PWI.nii';scaled_pwi.descript = 'Scaled from the PWI Image';pwi_data = spm_read_vols(raw_pwi);Lamda = 0.9000;Alpha = 0.9500;Tau = 22.50;R1A = (1684)^-1;PER100G = 100;SEC_PER_MIN = 60;MSEC_PER_SEC = 1000;TI1 = 700;TI2 = 1800;PWI_scale = zeros(size(pwi_data));sliceNumbers = (1:size(pwi_data, 3))';Constant = Lamda / (2 * Alpha * TI1) * (PER100G * SEC_PER_MIN * MSEC_PER_SEC);Slice_based_const = exp(R1A * (TI2 + (sliceNumbers - 1) * Tau));Numerator = pwi_data;for n =1:size(sliceNumbers); PWI_scale(:,:,n) = Constant * Slice_based_const(n) * Numerator(:,:,n);end; spm_write_vol(scaled_pwi, PWI_scale);" % (
all_aligned_dir)
mlc.inputs.script = cmd
out = mlc.run()
def mat_to_nii(mat_roi_path):
import nipype.interfaces.matlab as matlab
import os
mlab = matlab.MatlabCommand()
mlab.inputs.script = """
marsbar on
load %s
save_as_image(roi, '%s')
""" % (mat_roi_path, mat_roi_path.strip('_roi.mat') + '.nii')
mlab.run()
def test_run_interface():
default_script_file = clean_workspace_and_get_default_script_file()
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
assert not os.path.exists(
default_script_file), 'scriptfile should not exist 1.'
with pytest.raises(ValueError):
mc.run() # script is mandatory
assert not os.path.exists(
default_script_file), 'scriptfile should not exist 2.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
mc.inputs.script = 'a=1;'
assert not os.path.exists(
default_script_file), 'scriptfile should not exist 3.'
with pytest.raises(IOError):
mc.run() # foo_m is not an executable
assert os.path.exists(default_script_file), 'scriptfile should exist 3.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
cwd = os.getcwd()
basedir = mkdtemp()
os.chdir(basedir)
# bypasses ubuntu dash issue
mc = mlab.MatlabCommand(script='foo;', paths=[basedir], mfile=True)
assert not os.path.exists(
default_script_file), 'scriptfile should not exist 4.'
with pytest.raises(RuntimeError):
mc.run()
assert os.path.exists(default_script_file), 'scriptfile should exist 4.'
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
# bypasses ubuntu dash issue
res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run()
assert res.runtime.returncode == 0
assert os.path.exists(default_script_file), 'scriptfile should exist 5.'
os.chdir(cwd)
rmtree(basedir)
def ExploreDTI_tractography(flipped_mat):
import nipype.interfaces.matlab as Matlab
import os
from shutil import copy
import re
matlab = Matlab.MatlabCommand()
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
matlab.inputs.script = """
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Tractography%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
params.SeedPointRes = [2 2 2]
params.LinearGeoTrackRange = [0 1]
params.SphericalGeoTrackRange = [0 1]
params.InterpolationMethod = 1
params.PlanarGeoTrackRange = [0 1]
params.SeedFAThresh = 0.2
params.AngleThresh = 30
params.MDTrackRange = [0 Inf]
params.FiberLengthRange = [5 500]
params.ran_sam = 0
params.StepSize = 1
params.FAThresh = 0.2
params.SeedFAThreshold = 0.2
params.FATrackRange = [0.2 1]
tracts_thick = ['{0}/Diff_Multishell_{1}_Tracts_Thick.mat']
tracts_thin = ['{0}/Diff_Multishell_{1}_Tracts_Thin.mat']
%on the other hand, this will return only the major bundles
E_DTI_WholeBrainTracking('{2}', tracts_thick, params)
% params.FiberLengthRange = [50 500]
% this will written only the major tracts
% WholeBrainTrackingDTI_fast('{2}', tracts_thin, params)
""".format(
cwd, subj_no, flipped_mat
) #Ihave no idea why '' solved the problem of writing to different dir, but it did
res = matlab.run()
tracts = os.path.abspath(
'Diff_Multishell_{0}_Tracts_Thick.mat'.format(subj_no))
return tracts #You always need return
def test_run_interface(tmpdir):
default_script_file = clean_workspace_and_get_default_script_file()
mc = mlab.MatlabCommand(matlab_cmd="foo_m")
assert not os.path.exists(
default_script_file), "scriptfile should not exist 1."
with pytest.raises(ValueError):
mc.run() # script is mandatory
assert not os.path.exists(
default_script_file), "scriptfile should not exist 2."
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
mc.inputs.script = "a=1;"
assert not os.path.exists(
default_script_file), "scriptfile should not exist 3."
with pytest.raises(IOError):
mc.run() # foo_m is not an executable
assert os.path.exists(default_script_file), "scriptfile should exist 3."
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
cwd = tmpdir.chdir()
# bypasses ubuntu dash issue
mc = mlab.MatlabCommand(script="foo;", paths=[tmpdir.strpath], mfile=True)
assert not os.path.exists(
default_script_file), "scriptfile should not exist 4."
with pytest.raises(OSError):
mc.run()
assert os.path.exists(default_script_file), "scriptfile should exist 4."
if os.path.exists(default_script_file): # cleanup
os.remove(default_script_file)
# bypasses ubuntu dash issue
res = mlab.MatlabCommand(script="a=1;", paths=[tmpdir.strpath],
mfile=True).run()
assert res.runtime.returncode == 0
assert os.path.exists(default_script_file), "scriptfile should exist 5."
cwd.chdir()
def ExploreDTI_sort(eddy_file):
import nipype.interfaces.matlab as Matlab
import os
import re
from shutil import copy
matlab = Matlab.MatlabCommand()
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
Bmatrix = '/media/amr/Amr_4TB/Work/October_Acquistion/Bmatrix_ExploreDTI.txt'
experiment_dir = '/media/amr/Amr_4TB/Work/October_Acquistion'
working_dir = 'Diffusion_Multishell_ExploreDTI_workingdir'
workflow = 'Multishell_ExploreDTI_workflow'
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
copy(
Bmatrix,
'%s/%s/%s/_subject_id_%s/decompress/Diff_Multishell_%s_edc_chdt.txt' %
(experiment_dir, working_dir, workflow, subj_no, subj_no))
matlab.inputs.script = """
eddy_file = '{0}'
name_wo_ext = eddy_file(145:end-4)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Sort eddy_corrected nii%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% You need the absolute path for things to work
E_DTI_sort_DWIs_wrt_b_val_ex(eddy_file,['{1}' '/' '' name_wo_ext '_sorted.nii'],...
['{1}' '/' '' name_wo_ext '_sorted.nii'])
""".format(
eddy_file, cwd
) #Ihave no idea why '' solved the problem of writing to different dir, but it did
res = matlab.run()
sorted_nii = os.path.abspath(
'Diff_Multishell_{0}_edc_chdt_sorted.nii'.format(subj_no))
sorted_txt = os.path.abspath(
'Diff_Multishell_{0}_edc_chdt_sorted.txt'.format(subj_no))
return sorted_nii, sorted_txt #You always need return
def check_system_spm_available():
"""Check SPM can be found by Matlab
Make sure SPM can be found by Matlab and terminate the program if it
cannot.
Args:
N/A
Returns:
spm_found (Boolean): True if SPM folder in Matlab path, False
otherwise
spm_path (string): path to the SPM folder found by Matlab.
Retrieved with the 'which spm' Matlab command.
None if not found
spmscript_path (string): path to the spm.m in the SPM folder
found by Matlab.
None if SPM folder not found.
"""
# initialise output variables
#-- SPM found boolean
spm_found = False
#-- SPM folder
spm_path = None
#-- SPM script ([folder]/spm.m)
spmscript_path = None
# Check if SPM path can be found by Matlab
# (e.g., if file $HOME/matlab/startup.m contains the line
# addpath [spm_folder])
res = mlab.MatlabCommand(script='which spm', mfile=False).run()
whichspm_output = res.runtime.stdout.splitlines()[-2]
if whichspm_output == '\'spm\' not found.':
#-- SPM found boolean
spm_found = False
#-- SPM folder
spm_path = None
#-- SPM script ([folder]/spm.m)
spmscript_path = None
else:
# SPM found
spm_found = True
spmscript_path = whichspm_output
spm_path = os.path.dirname(spmscript_path)
return spm_found, spm_path, spmscript_path
def NODDI(brain_nii, brain_mask_nii):
import os
import nipype.interfaces.matlab as Matlab
matlab = Matlab.MatlabCommand()
bval = '/media/amr/HDD/Work/October_Acquistion/bval_multishell'
bvec = '/media/amr/HDD/Work/October_Acquistion/bvec_multishell'
brain_mat_name = 'NODDI_brain.mat'
prefix = 'NODDI'
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
import os
matlab.inputs.script = """
bval = '/media/amr/HDD/Work/October_Acquistion/bval_multishell'
bvec = '/media/amr/HDD/Work/October_Acquistion/bvec_multishell'
brain_mat_name = 'NODDI_brain.mat'
prefix = 'NODDI'
CreateROI('%s', '%s', brain_mat_name);
protocol = FSL2Protocol('%s', '%s');
noddi = MakeModel('WatsonSHStickTortIsoV_B0');
batch_fitting_single(brain_mat_name, protocol, noddi, 'FittedParams.mat');
SaveParamsAsNIfTI('FittedParams.mat', brain_mat_name, '%s', prefix)
""" % (brain_nii, brain_mask_nii, bval, bvec, brain_mask_nii)
res = matlab.run()
odi = os.path.abspath('NODDI_odi.nii')
ficvf = os.path.abspath('NODDI_ficvf.nii')
return odi, ficvf
def test_cmdline():
default_script_file = clean_workspace_and_get_default_script_file()
mi = mlab.MatlabCommand(script='whos',
script_file='testscript', mfile=False)
yield assert_equal, mi.cmdline, \
matlab_cmd + (' -nodesktop -nosplash -singleCompThread -r "fprintf(1,'
'\'Executing code at %s:\\n\',datestr(now));ver,try,'
'whos,catch ME,fprintf(2,\'MATLAB code threw an '
'exception:\\n\');fprintf(2,\'%s\\n\',ME.message);if '
'length(ME.stack) ~= 0, fprintf(2,\'File:%s\\nName:%s\\n'
'Line:%d\\n\',ME.stack.file,ME.stack.name,'
'ME.stack.line);, end;end;;exit"')
yield assert_equal, mi.inputs.script, 'whos'
yield assert_equal, mi.inputs.script_file, 'testscript'
yield assert_false, os.path.exists(mi.inputs.script_file), 'scriptfile should not exist'
yield assert_false, os.path.exists(default_script_file), 'default scriptfile should not exist.'
def ExploreDTI_mat(sorted_nii, sorted_txt):
import nipype.interfaces.matlab as Matlab
import os
from shutil import copy
import re
matlab = Matlab.MatlabCommand()
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
matlab.inputs.script = """
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%convert to kurtosis.mat%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Mask_par.tune_NDWI = 0.7; % recommened by Leemans
Mask_par.tune_DWI = 0.7;
Mask_par.mfs = 5
f_DWI = '{0}'
f_BM = '{1}'
basename = f_DWI(1:end-4)
f_mat = [basename '.mat']
E_DTI_quick_and_dirty_DKI_convert_from_nii_txt_to_mat(f_DWI, f_BM, f_mat, Mask_par, 6, 2, 1)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Now flip R-L%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
flipped_mat = ['{2}/Diff_Multishell_{3}_sorted_flipped.mat']
E_DTI_Flip_left_right_mat(f_mat,flipped_mat)
""".format(
sorted_nii, sorted_txt, cwd, subj_no
) #Ihave no idea why '' solved the problem of writing to different dir, but it did
res = matlab.run()
flipped_mat = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped.mat'.format(subj_no))
return flipped_mat #You always need return
def test_cmdline():
basedir = mkdtemp()
mi = mlab.MatlabCommand(script='whos',
script_file='testscript',
mfile=False)
yield assert_equal, mi.cmdline, \
matlab_cmd + (' -nodesktop -nosplash -singleCompThread -r "fprintf(1,'
'\'Executing code at %s:\\n\',datestr(now));ver,try,'
'whos,catch ME,fprintf(2,\'MATLAB code threw an '
'exception:\\n\');fprintf(2,\'%s\\n\',ME.message);if '
'length(ME.stack) ~= 0, fprintf(2,\'File:%s\\nName:%s\\n'
'Line:%d\\n\',ME.stack.file,ME.stack.name,'
'ME.stack.line);, end;end;;exit"')
yield assert_equal, mi.inputs.script, 'whos'
yield assert_equal, mi.inputs.script_file, 'testscript'
path_exists = os.path.exists(os.path.join(basedir, 'testscript.m'))
yield assert_false, path_exists
rmtree(basedir)
def apply_transform_onefile(transform, file):
""" applies transform to files using spm """
startdir = os.getcwd()
pth, _ = os.path.split(file)
os.chdir(pth)
mlab_cmd = mlab.MatlabCommand(matlab_cmd='matlab-spm8')
mlab_cmd.inputs.nodesktop = True
mlab_cmd.inputs.nosplash = True
mlab_cmd.inputs.ignore_exception = True
mlab_cmd.inputs.mfile = True
mlab_cmd.inputs.script_file = 'pyspm8_apply_transform.m'
script = """
infile = \'%s\';
transform = load(\'%s\');
imgspace = spm_get_space(infile);
spm_get_space(infile ,transform.M*imgspace);
""" % (file, transform)
mlab_cmd.inputs.script = script
mout = mlab_cmd.run()
os.chdir(startdir)
return mout
def spm_get_space(in_file):
"""Run the spm function spm_get_space through Matlab.
Parameters
==========
in_file : str
Path to an existant nifti image.
Returns
=======
affine : numpy.ndarray of shape (4, 4)
The affine transformation matrix.
"""
mat_path = '/tmp/space.mat'
mlab = matlab.MatlabCommand()
mlab.inputs.script = "\naddpath '/i2bm/local/spm8-6313/' \n" + \
"matrix = spm_get_space(" + in_file + ");\n" + \
"save('" + mat_path + "', 'matrix')"
mlab.run()
mat_dict = loadmat(mat_path)
affine = mat_dict['matrix']
return affine
def test_cmdline():
default_script_file = clean_workspace_and_get_default_script_file()
mi = mlab.MatlabCommand(script="whos",
script_file="testscript",
mfile=False)
assert mi.cmdline == matlab_cmd + (
' -nodesktop -nosplash -singleCompThread -r "fprintf(1,'
"'Executing code at %s:\\n',datestr(now));ver,try,"
"whos,catch ME,fprintf(2,'MATLAB code threw an "
"exception:\\n');fprintf(2,'%s\\n',ME.message);if "
"length(ME.stack) ~= 0, fprintf(2,'File:%s\\nName:%s\\n"
"Line:%d\\n',ME.stack.file,ME.stack.name,"
'ME.stack.line);, end;end;;exit"')
assert mi.inputs.script == "whos"
assert mi.inputs.script_file == "testscript"
assert not os.path.exists(
mi.inputs.script_file), "scriptfile should not exist"
assert not os.path.exists(
default_script_file), "default scriptfile should not exist."
def ExploreDTI_calculate_tracts_from_masks(cwd_masks, tracts, mat):
import nipype.interfaces.matlab as Matlab
import os
from shutil import copy
import re
matlab = Matlab.MatlabCommand()
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
matlab.inputs.script = """
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%calculate tracts from masks%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
E_DTI_Analyse_tracts_ff...
('{0}', '{1}', '{2}', '{3}/CC_Tracts_{4}.mat')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Extract Tract Info%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
E_DTI_Convert_Tract_mats_2_xls('{3}', '{3}/Tracts_Desc_Stats_{4}.csv')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Extract Tract Info Other Modalities%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Native space, do not forget
% put all images you wish to extract tract info from
% matlab from inside python does not accept curly braces aka cells, i tried many combinations without much luck
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Diff_20
fa_diff_20 = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_20_workingdir/DTI_workflow/_subject_id_{4}/fit_tensor/dtifit__FA.nii.gz'
E_DTI_Export_Tract_Volume_Info(fa_diff_20 ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
fa_diff_20 = load('{3}/CC_Tracts_{4}_dtifit__FA.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FA_Diff_20_{4},' num2str(fa_diff_20.mean_TV)], 'delimiter','','-append');
md_diff_20 = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_20_workingdir/DTI_workflow/_subject_id_{4}/fit_tensor/dtifit__MD.nii.gz'
E_DTI_Export_Tract_Volume_Info(md_diff_20 ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
md_diff_20 = load('{3}/CC_Tracts_{4}_dtifit__MD.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MD_Diff_20_{4},' num2str(md_diff_20.mean_TV)], 'delimiter','','-append');
ad_diff_20 = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_20_workingdir/DTI_workflow/_subject_id_{4}/fit_tensor/dtifit__L1.nii.gz'
E_DTI_Export_Tract_Volume_Info(ad_diff_20 ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
ad_diff_20 = load('{3}/CC_Tracts_{4}_dtifit__L1.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AD_Diff_20_{4},' num2str(ad_diff_20.mean_TV)], 'delimiter','','-append');
rd_diff_20 = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_20_workingdir/DTI_workflow/_subject_id_{4}/RD/dtifit__L2_maths_maths.nii.gz'
E_DTI_Export_Tract_Volume_Info(rd_diff_20 ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
rd_diff_20 = load('{3}/CC_Tracts_{4}_dtifit__L2_maths_maths.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RD_Diff_20_{4},' num2str(rd_diff_20.mean_TV)], 'delimiter','','-append');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CHARMED
FA_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/Tensor.FA.nii.gz'
E_DTI_Export_Tract_Volume_Info(FA_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
FA_CHARMED = load('{3}/CC_Tracts_{4}_Tensor.FA.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FA_CHARMED_{4},' num2str(FA_CHARMED.mean_TV)], 'delimiter','','-append');
MD_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/Tensor.MD.nii.gz'
E_DTI_Export_Tract_Volume_Info(MD_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
MD_CHARMED = load('{3}/CC_Tracts_{4}_Tensor.MD.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MD_CHARMED_{4},' num2str(MD_CHARMED.mean_TV)], 'delimiter','','-append');
AD_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/Tensor.AD.nii.gz'
E_DTI_Export_Tract_Volume_Info(AD_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AD_CHARMED = load('{3}/CC_Tracts_{4}_Tensor.AD.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AD_CHARMED_{4},' num2str(AD_CHARMED.mean_TV)], 'delimiter','','-append');
RD_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/Tensor.RD.nii.gz'
E_DTI_Export_Tract_Volume_Info(RD_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
RD_CHARMED = load('{3}/CC_Tracts_{4}_Tensor.RD.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RD_CHARMED_{4},' num2str(RD_CHARMED.mean_TV)], 'delimiter','','-append');
FR_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/FR.nii.gz'
E_DTI_Export_Tract_Volume_Info(FR_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
FR_CHARMED = load('{3}/CC_Tracts_{4}_FR.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FR_CHARMED_{4},' num2str(FR_CHARMED.mean_TV)], 'delimiter','','-append');
IAD_CHARMED = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_CHARMED_workingdir/Multishell_CHARMED_workflow/_subject_id_{4}/CHARMED_r2/CHARMED_r2/CHARMEDRestricted0.d.nii.gz'
E_DTI_Export_Tract_Volume_Info(IAD_CHARMED ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
IAD_CHARMED = load('{3}/CC_Tracts_{4}_CHARMEDRestricted0.d.nii_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['IAD_CHARMED_{4},' num2str(IAD_CHARMED.mean_TV)], 'delimiter','','-append');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%NODDI
ODI_NODDI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_NODDI_workingdir/Multishell_NODDI_workflow/_subject_id_{4}/NODDI/NODDI_odi.nii'
E_DTI_Export_Tract_Volume_Info(ODI_NODDI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
ODI_NODDI = load('{3}/CC_Tracts_{4}_NODDI_odi_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['ODI_NODDI_{4},' num2str(ODI_NODDI.mean_TV)], 'delimiter','','-append');
FICVF_NODDI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_NODDI_workingdir/Multishell_NODDI_workflow/_subject_id_{4}/NODDI/NODDI_ficvf.nii'
E_DTI_Export_Tract_Volume_Info(FICVF_NODDI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
FICVF_NODDI = load('{3}/CC_Tracts_{4}_NODDI_ficvf_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FICVF_NODDI_{4},' num2str(FICVF_NODDI.mean_TV)], 'delimiter','','-append');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Kurtosis_dipy
FA_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_FA.nii'
E_DTI_Export_Tract_Volume_Info(FA_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
FA_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_FA_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FA_Kurtosis_dipy_{4},' num2str(FA_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
MD_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_MD.nii'
E_DTI_Export_Tract_Volume_Info(MD_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
MD_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_MD_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MD_Kurtosis_dipy_{4},' num2str(MD_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
AD_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_AD.nii'
E_DTI_Export_Tract_Volume_Info(AD_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AD_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_AD_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AD_Kurtosis_dipy_{4},' num2str(AD_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
RD_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_RD.nii'
E_DTI_Export_Tract_Volume_Info(RD_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
RD_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_RD_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RD_Kurtosis_dipy_{4},' num2str(RD_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
AK_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_AK.nii'
E_DTI_Export_Tract_Volume_Info(AK_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AK_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_AK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AK_Kurtosis_dipy_{4},' num2str(AK_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
AWF_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_AWF.nii'
E_DTI_Export_Tract_Volume_Info(AWF_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AWF_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_AWF_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AWF_Kurtosis_dipy_{4},' num2str(AWF_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
MK_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_MK.nii'
E_DTI_Export_Tract_Volume_Info(MK_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
MK_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_MK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MK_Kurtosis_dipy_{4},' num2str(MK_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
RK_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_RK.nii'
E_DTI_Export_Tract_Volume_Info(RK_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
RK_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_RK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RK_Kurtosis_dipy_{4},' num2str(RK_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
TORT_Kurtosis_dipy = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_Kurtosis_workingdir/Multishell_workflow_Kurtosis/_subject_id_{4}/Kurtosis/DKI_TORT.nii'
E_DTI_Export_Tract_Volume_Info(TORT_Kurtosis_dipy ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
TORT_Kurtosis_dipy = load('{3}/CC_Tracts_{4}_DKI_TORT_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['TORT_Kurtosis_dipy_{4},' num2str(TORT_Kurtosis_dipy.mean_TV)], 'delimiter','','-append');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Kurtosis_ExploreDTI
FA_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_FA.nii'
E_DTI_Export_Tract_Volume_Info(FA_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
FA_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_FA_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['FA_Kurtosis_E_DTI_{4},' num2str(FA_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
MD_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_MD.nii'
E_DTI_Export_Tract_Volume_Info(MD_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
MD_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_MD_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MD_Kurtosis_E_DTI_{4},' num2str(MD_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
AD_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_L1.nii'
E_DTI_Export_Tract_Volume_Info(AD_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AD_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_L1_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AD_Kurtosis_E_DTI_{4},' num2str(AD_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
RD_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_RD.nii'
E_DTI_Export_Tract_Volume_Info(RD_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
RD_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_RD_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RD_Kurtosis_E_DTI_{4},' num2str(RD_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
AK_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_AK.nii'
E_DTI_Export_Tract_Volume_Info(AK_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AK_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_AK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AK_Kurtosis_E_DTI_{4},' num2str(AK_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
AWF_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_AWF.nii'
E_DTI_Export_Tract_Volume_Info(AWF_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
AWF_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_AWF_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['AWF_Kurtosis_E_DTI_{4},' num2str(AWF_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
KA_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_KA.nii'
E_DTI_Export_Tract_Volume_Info(KA_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
KA_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_KA_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['KA_Kurtosis_E_DTI_{4},' num2str(KA_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
MK_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_MK.nii'
E_DTI_Export_Tract_Volume_Info(MK_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
MK_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_MK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['MK_Kurtosis_E_DTI_{4},' num2str(MK_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
RK_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_RK.nii'
E_DTI_Export_Tract_Volume_Info(RK_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
RK_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_RK_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['RK_Kurtosis_E_DTI_{4},' num2str(RK_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
TORT_Kurtosis_E_DTI = '/media/amr/Amr_4TB/Work/October_Acquistion/Diffusion_Multishell_ExploreDTI_workingdir/Multishell_ExploreDTI_workflow/_subject_id_{4}/ExploreDTI_kurtosis/Diff_Multishell_{4}_sorted_flipped_TORT.nii'
E_DTI_Export_Tract_Volume_Info(TORT_Kurtosis_E_DTI ,'{3}/CC_Tracts_{4}.mat','{2}','{3}')
TORT_Kurtosis_E_DTI = load('{3}/CC_Tracts_{4}_Diff_Multishell_{4}_sorted_flipped_TORT_Vol_Info.mat');
dlmwrite('{3}/Tracts_Others_Stats_{4}.csv', ['TORT_Kurtosis_E_DTI_{4},' num2str(TORT_Kurtosis_E_DTI.mean_TV)], 'delimiter','','-append');
""".format(
cwd_masks, tracts, mat, cwd, subj_no
) #Ihave no idea why '' solved the problem of writing to different dir, but it did
res = matlab.run()
cc_tracts = os.path.abspath('CC_Tracts_{0}.mat'.format(subj_no))
return cc_tracts #You always need return
def ExploreDTI_kurtosis(flipped_mat):
import nipype.interfaces.matlab as Matlab
import os
from shutil import copy
import re
matlab = Matlab.MatlabCommand()
# below is where you add paths that matlab might require, this is equivalent to addpath()
matlab.inputs.paths = ['/home/amr/SCRIPTS/']
matlab.inputs.single_comp_thread = False
cwd = os.getcwd()
subj_no = re.findall('\d+', cwd)[-1]
matlab.inputs.script = """
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Get Kurtosis params%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
addpath('/media/amr/HDD/Softwares/ExploreDTI')
MainExploreDTI;
vars = E_DTI_Complete_List_var;
% FA -> 1
% MD -> 2
% L1 aka AD ->3
% RD -> 6
%
% 'Mean kurtosis (''_MK.nii'')' -> 46
% 'Axial kurtosis (''_AK.nii'')' -> 47
% 'Radial kurtosis (''_RK.nii'')' -> 48
% 'Kurtosis anisotropy (''_KA.nii'')' -> 49
% AWF -> 53
% TORT -> 54
E_DTI_Convert_mat_2_nii('{0}', '{1}', vars([1:3,6,46:49,53,54]))
""".format(
flipped_mat, cwd
) #Ihave no idea why '' solved the problem of writing to different dir, but it did
res = matlab.run()
ak = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_AK.nii'.format(subj_no))
awf = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_AWF.nii'.format(subj_no))
fa = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_FA.nii'.format(subj_no))
ka = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_KA.nii'.format(subj_no))
ad = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_L1.nii'.format(subj_no))
md = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_MD.nii'.format(subj_no))
mk = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_MK.nii'.format(subj_no))
rd = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_RD.nii'.format(subj_no))
rk = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_RK.nii'.format(subj_no))
tort = os.path.abspath(
'Diff_Multishell_{0}_sorted_flipped_TORT.nii'.format(subj_no))
return ak, awf, fa, ka, ad, md, mk, rd, rk, tort #You always need return
def test_set_matlabcmd():
mi = mlab.MatlabCommand()
mi.set_default_matlab_cmd('foo')
yield assert_equal, mi._default_matlab_cmd, 'foo'
mi.set_default_matlab_cmd(matlab_cmd)
