def test_ae(
filename='/Volumes/VAULT/YOAD/all/01-001.fmri.rest.1.volreg.band.nii.gz',
filename_mask='/Volumes/VAULT/YOAD/all/registrations/01-001.fmri.rest.1.volreg.cortical_mask.nii.gz'
):
img = Image(img_filename=filename, mask_filename=filename_mask)
xmat = img.image_mat_in_mask_normalised.T
ae = Autoencoder(30, max_iter=200, second_nonlinear=True,
bias=True).fit(xmat)
img.write_decomposition(maps=ae.components_,
filename='test_ae.nii.gz',
normalise=False)
def test_infomax(
filename='./data/01-001.fmri.rest.1.volreg.band.pca_reduced.nii.gz',
filename_mask='./data/01-001.fmri.rest.1.volreg.cortical_mask.nii.gz'):
from Image import Image
from sklearn.decomposition import FastICA
import scipy.io as sio
img = Image(img_filename=filename, mask_filename=filename_mask, fwhm=6.0)
xmat = img.image_mat_in_mask_normalised.T
from InfoMax import InfoMax
infomax = InfoMax(30).fit(xmat)
img.write_decomposition(maps=infomax.components_,
filename='test_ica_infomax.nii.gz',
normalise=True)
def test_rica(
filename='./data/01-001.fmri.rest.1.volreg.nii.gz',
filename_mask='./data/01-001.fmri.rest.1.volreg.cortical_mask.nii.gz'):
from Image import Image
import scipy.io as sio
img = Image(img_filename=filename, mask_filename=filename_mask)
xmat = img.image_mat_in_mask_normalised.T
from sklearn.decomposition import PCA, FastICA
pca = PCA(30)
xmat_red = pca.fit_transform(xmat.T)
import matplotlib.pyplot as plt
plt.plot(pca.components_.T)
plt.show()
import pdb
pdb.set_trace()
rica = RICA(30).fit(xmat)
img.write_decomposition(maps=rica.components_,
filename='test_rica.nii.gz',
normalise=False)
def fmri(fmri_collection,
t1_collection=None,
seg_collections=None,
atlas_collections=None,
directory_reg=None,
freq_band="0.01 0.1"):
if directory_reg:
call("mkdir -p {directory_reg}".format(directory_reg=directory_reg),
shell=True)
for index, fmri_scan in enumerate(fmri_collection):
id_start = fmri_scan.rfind('/') + 1
id_end = fmri_scan.find('.')
directory = fmri_scan[0:id_start]
identifier = fmri_scan[id_start:id_end]
# distortion correction if still required - deprecated
VOLUMES = check_output('3dinfo -nv {scan}'.format(scan=fmri_scan),
shell=True).rstrip()
TR = check_output('3dinfo -tr {scan}'.format(scan=fmri_scan),
shell=True).rstrip()
print "scan: {scan} TR={TR} VOLUMES={VOLUMES}".format(scan=identifier,
TR=TR,
VOLUMES=VOLUMES)
##########################################################################################################
################################# FILE SETUP #############################################################
##########################################################################################################
### 3ddespike
in_3ddespike = fmri_scan
out_3ddespike = "{directory}{fmri_id}.fmri.despike.nii.gz".format(
fmri_id=identifier, directory=directory)
### 3dvolreg
in_3dvolreg = out_3ddespike
out_3dvolreg = "{prefix}.volreg.nii.gz".format(prefix=in_3dvolreg[:-7])
out_3dvolreg_txt = "{directory}{fmri_id}.motion.1D".format(
fmri_id=identifier, directory=directory)
out_motion = "{directory}{fmri_id}.motion.demean.1D".format(
fmri_id=identifier, directory=directory)
out_motion_derv = "{directory}{fmri_id}.motion.demean.derivative.1D".format(
fmri_id=identifier, directory=directory)
### 3dvol to extract 4th volume
in_3dvol = out_3dvolreg
out_3dvol = "{prefix}.vol4.nii.gz".format(prefix=in_3dvol[:-7])
### fmri brain mask
in_3dAutomask = out_3dvolreg
out_3dAutomask = "{prefix}.mask.nii.gz".format(prefix=out_3dvol[:-7])
### 3dBandpass
in_3dBandpass = out_3dvolreg
out_3dBandpass = "******".format(
prefix=in_3dBandpass[:-7])
out_3dBandpass_regressors = "{directory}{fmri_id}.bandpass.1D".format(
fmri_id=identifier, directory=directory)
### 3dDeconvolve
in_3dDeconvolve = out_3dvolreg
out_3dDeconvolve_err = "{prefix}.deconvolve.err.nii.gz".format(
prefix=in_3dDeconvolve[:-7])
out_3dDeconvolve_fit = "{prefix}.deconvolve.fit.nii.gz".format(
prefix=in_3dDeconvolve[:-7])
out_3dDeconvolve_stats = "{prefix}.deconvolve.stats.nii.gz".format(
prefix=in_3dDeconvolve[:-7])
### final output
fmri_preprocessed = out_3dDeconvolve_err
fvol = out_3dvol
matching_t1 = [s for s in t1_collection if identifier in s]
matching_seg = [s for s in seg_collections if identifier in s]
matching_atlas = [s for s in atlas_collections if identifier in s]
if len(matching_t1) > 0:
t1 = matching_t1[0]
aff_t1_2_fmri = "{directory_reg}{fmri_id}.t1__2__{fmri_id}.fmri.despike.volreg.vol4.txt".format(
fmri_id=identifier, directory_reg=directory_reg)
aff_fmri_2_t1 = "{directory_reg}{fmri_id}.fmri.despike.volreg.vol4__2__{fmri_id}.t1.txt".format(
fmri_id=identifier, directory_reg=directory_reg)
aff_t1_in_fmri = "{directory_reg}{fmri_id}.t1__in__{fmri_id}.fmri.despike.volreg.vol4.nii.gz".format(
fmri_id=identifier, directory_reg=directory_reg)
aff_fmri_in_t1 = "{directory_reg}{fmri_id}.fmri.despike.volreg.vol4__in__{fmri_id}.t1.nii.gz".format(
fmri_id=identifier, directory_reg=directory_reg)
if len(matching_seg) > 0 and len(matching_atlas) > 0:
seg = matching_seg[0]
atlas = matching_atlas[0]
fmri_seg = "{directory}{fmri_id}.fmri.despike.volreg.vol4.seg.nii.gz".format(
directory=directory, fmri_id=identifier)
fmri_atlas = "{directory}{fmri_id}.fmri.despike.volreg.vol4.atlas.nii.gz".format(
directory=directory, fmri_id=identifier)
##########################################################################################################
################################# FMRI PREPROCESSING #####################################################
##########################################################################################################
# despiking
if not isfile(out_3ddespike):
cmd = "3dDespike -NEW -nomask -prefix {out_} {in_}".format(
in_=in_3ddespike, out_=out_3ddespike)
print cmd
call(cmd, shell=True)
# motion realignment
if not isfile(out_3dvolreg):
cmd = "3dvolreg -overwrite -zpad 1 -cubic -prefix {out_} -1Dfile {out_txt} {in_}".format(
out_txt=out_3dvolreg_txt, in_=in_3dvolreg, out_=out_3dvolreg)
print cmd
call(cmd, shell=True)
cmd = "1d_tool.py -infile {in_} -set_nruns 1 -demean -write {out_}".format(
in_=out_3dvolreg_txt, out_=out_motion)
print cmd
call(cmd, shell=True)
cmd = "1d_tool.py -infile {in_} -set_nruns 1 -derivative -demean -write {out_}".format(
in_=out_3dvolreg_txt, out_=out_motion_derv)
print cmd
call(cmd, shell=True)
# get one volume
if not isfile(out_3dvol):
cmd = "3dcalc -overwrite -a '{in_}[4]' -prefix {out_} -expr a".format(
in_=in_3dvol, out_=out_3dvol)
call(cmd, shell=True)
# get brain mask for volume
if not isfile(out_3dAutomask):
cmd = "3dAutomask -overwrite -prefix {out_} {in_}".format(
in_=in_3dAutomask, out_=out_3dAutomask)
call(cmd, shell=True)
# band passs filter signals
if not isfile(out_3dBandpass_regressors):
#cmd = "3dBandpass -overwrite -band 0.01 0.1 -prefix {out_} {in_}".format(in_=in_3dBandpass, out_=out_3dBandpass)
cmd = "1dBport -nodata {VOLUMES} {TR} -band {band} -invert -nozero > {out_}".format(
VOLUMES=VOLUMES,
TR=TR,
out_=out_3dBandpass_regressors,
band=freq_band)
print cmd
call(cmd, shell=True)
if not isfile(out_3dDeconvolve_err):
cmd = """3dDeconvolve -input {in_} \
-ortvec {bandpass} bandpass \
-polort 3 \
-num_stimts 12 \
-stim_file 1 {motion}'[0]' -stim_base 1 -stim_label 1 roll_01 \
-stim_file 2 {motion}'[1]' -stim_base 2 -stim_label 2 pitch_01 \
-stim_file 3 {motion}'[2]' -stim_base 3 -stim_label 3 yaw_01 \
-stim_file 4 {motion}'[3]' -stim_base 4 -stim_label 4 dS_01 \
-stim_file 5 {motion}'[4]' -stim_base 5 -stim_label 5 dL_01 \
-stim_file 6 {motion}'[5]' -stim_base 6 -stim_label 6 dP_01 \
-stim_file 7 {motion_derv}'[0]' -stim_base 7 -stim_label 7 roll_02 \
-stim_file 8 {motion_derv}'[1]' -stim_base 8 -stim_label 8 pitch_02 \
-stim_file 9 {motion_derv}'[2]' -stim_base 9 -stim_label 9 yaw_02 \
-stim_file 10 {motion_derv}'[3]' -stim_base 10 -stim_label 10 dS_02 \
-stim_file 11 {motion_derv}'[4]' -stim_base 11 -stim_label 11 dL_02 \
-stim_file 12 {motion_derv}'[5]' -stim_base 12 -stim_label 12 dP_02 \
-fitts {out_fit} \
-errts {out_err} \
-bucket {out_stats} """.format(in_=in_3dDeconvolve,
bandpass=out_3dBandpass_regressors,
motion=out_motion,
motion_derv=out_motion_derv,
out_fit=out_3dDeconvolve_fit,
out_err=out_3dDeconvolve_err,
out_stats=out_3dDeconvolve_stats)
call(cmd, shell=True)
#########################################################################################################################################
################################################### AFFINE REGISTRATIONS ################################################################
#########################################################################################################################################
#(i) fmri to t1
if t1 and atlas and not isfile(aff_fmri_in_t1):
cmd = "reg_aladin -ref {ref} -rmask {rmask} -flo {flo} -fmask {fmask} -res {res} -aff {aff}".format(
ref=t1,
flo=fvol,
res=aff_fmri_in_t1,
aff=aff_fmri_2_t1,
rmask=atlas,
fmask=out_3dAutomask)
print cmd
call(cmd, shell=True)
#(ii) t1 to fmri
if t1 and atlas and not isfile(aff_t1_in_fmri):
cmd = "reg_aladin -ref {ref} -rmask {rmask} -flo {flo} -fmask {fmask} -res {res} -aff {aff}".format(
ref=fvol,
flo=t1,
res=aff_t1_in_fmri,
aff=aff_t1_2_fmri,
fmask=atlas,
rmask=out_3dAutomask)
print cmd
call(cmd, shell=True)
# resample seg in fmri space
if seg and not isfile(fmri_seg):
cmd = "reg_resample -ref {ref} -flo {flo} -psf -res {res} -trans {trans}".format(
ref=fvol, flo=seg, res=fmri_seg, trans=aff_t1_2_fmri)
print cmd
call(cmd, shell=True)
# resample atlas in fmri space
if atlas and not isfile(fmri_atlas):
cmd = "reg_resample -ref {ref} -flo {flo} -inter 0 -res {res} -trans {trans}".format(
ref=fvol, flo=atlas, res=fmri_atlas, trans=aff_t1_2_fmri)
print cmd
call(cmd, shell=True)
# build atlas based correlation matrices
img = Image(img_filename=fmri_preprocessed,
mask_filename=fmri_atlas,
atlas_filename=fmri_atlas,
atlas_thr=1)
sio.savemat(
"{prefix}.corr.mat".format(prefix=fmri_preprocessed[:-7]),
{'CorrMatrix': img.atlas_corr})
sio.savemat(
"{prefix}.rois.mat".format(prefix=fmri_preprocessed[:-7]),
{'ROISignals': img.image_mat_in_mask_normalised_atlas})
labels = np.unique(img.atlas_v)
labels = labels[labels > 0]
sio.savemat(
"{prefix}.rois_label.mat".format(
prefix=fmri_preprocessed[:-7]), {'ROILabels': labels})
from niftybold.img.Image import Image
import scipy.io as sio
import argparse
import numpy as np
parser = argparse.ArgumentParser(description='build nifti file from mat file')
parser.add_argument('-img', metavar='img', type=str, required=True)
parser.add_argument('-mask', metavar='mask', type=str, required=True)
parser.add_argument('-mat', metavar='mat', type=str, required=True)
parser.add_argument('-normalise',
metavar='normalises',
type=bool,
default=False)
args = parser.parse_args()
f = sio.loadmat(args.mat)
hiddenlayer = f['h']
img = Image(img_filename=args.img, mask_filename=args.mask)
img.write_decomposition(maps=hiddenlayer,
filename="{prefix}.nii.gz".format(
prefix=args.mat[0:args.mat.find('.mat')]),
normalise=args.normalise)
from niftybold.img.Image import Image
import scipy.io as sio
import argparse
import numpy as np
parser = argparse.ArgumentParser(description='build mat file from nifti file')
parser.add_argument('-img', metavar='img', type=str, required=True)
parser.add_argument('-mask', metavar='mask', type=str, required=True)
parser.add_argument('-mat', metavar='mat', type=str, required=True)
parser.add_argument('-normalise',
metavar='normalises',
type=bool,
default=True)
parser.add_argument('-asl', metavar='asl', type=bool, default=False)
parser.add_argument('-fwhm', metavar='fwhm', type=float, default=0.0)
args = parser.parse_args()
img = Image(img_filename=args.img,
mask_filename=args.mask,
fwhm=args.fwhm,
asl=args.asl)
if args.normalise:
_mat = img.image_mat_in_mask_normalised.T
else:
_mat = img.image_mat_in_mask.T
sio.savemat(args.mat, {'mat': _mat})
import argparse
import numpy as np
parser = argparse.ArgumentParser(
description='build mat file for matrix decomposition')
parser.add_argument('-groupimg',
metavar='groupimg',
type=str,
nargs='+',
required=True)
parser.add_argument('-groupmask', metavar='groupmask', type=str, required=True)
parser.add_argument('-fwhm', metavar='fwhm', type=float, default=0.0)
parser.add_argument('-mat', metavar='mat', type=str, default='ica_ready.mat')
args = parser.parse_args()
mat = None
for index, scan in enumerate(args.groupimg):
print scan
img = Image(img_filename=scan,
mask_filename=args.groupmask,
fwhm=args.fwhm)
_mat = img.image_mat_in_mask_normalised.T
sio.savemat("{prefix}.mat".format(prefix=scan[0:scan.find('.nii')]),
{'mat': _mat})
if index == 0:
mat = _mat
else:
mat = np.concatenate((mat, _mat))
sio.savemat(args.mat, {'mat': mat})
