def track(dname, fdwi, fbval, fbvec, fmask=None, seed_density=1, show=False):
data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
if fmask is None:
from dipy.segment.mask import median_otsu
b0_mask, mask = median_otsu(
data) # TODO: check parameters to improve the mask
else:
mask, mask_affine = load_nifti(fmask)
mask = np.squeeze(mask) #fix mask dimensions
# compute DTI model
from dipy.reconst.dti import TensorModel
tenmodel = TensorModel(gtab) #, fit_method='OLS') #, min_signal=5000)
# fit the dti model
tenfit = tenmodel.fit(data, mask=mask)
# save fa
ffa = dname + 'tensor_fa.nii.gz'
fa_img = nib.Nifti1Image(tenfit.fa.astype(np.float32), affine)
nib.save(fa_img, ffa)
sh_order = 8 #TODO: check what that does
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
'compute fiber ODFs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
# compute the response equation ?
from dipy.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere('symmetric362')
#TODO: check what that does
peaks_csd = peaks_from_model(
model=tenmodel,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5, #.5
min_separation_angle=25,
mask=mask,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
fpeaks = dname + 'peaks.npz'
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import (ThresholdTissueClassifier, LocalTracking)
stopping_thr = 0.25 #0.25
pam = load_peaks(fpeaks)
#ffa = dname + 'tensor_fa_nomask.nii.gz'
fa, fa_affine = load_nifti(ffa)
classifier = ThresholdTissueClassifier(fa, stopping_thr)
# seeds
seed_mask = fa > 0.4 #0.4 #TODO: check this parameter
seeds = utils.seeds_from_mask(seed_mask,
density=seed_density,
affine=affine)
# tractography, if affine then in world coordinates
streamlines = LocalTracking(pam,
classifier,
seeds,
affine=affine,
step_size=.5)
# Compute streamlines and store as a list.
streamlines = list(streamlines)
ftractogram = dname + 'tractogram.trk'
#save .trk
save_trk_old_style(ftractogram, streamlines, affine, fa.shape)
if show:
#render
show_results(data, streamlines, fa, fa_affine)
def simple_viewer(streamlines, vol, affine):
from dipy.viz import actor, window
renderer = window.Renderer()
renderer.add(actor.line(streamlines))
renderer.add(actor.slicer(vol, affine))
window.show(renderer)
dname = '/Users/ghfc/Desktop/Celine/brainhack/data/'
fdwi = dname + '2dseq_conv_32.nii.gz'
data, affine = load_nifti(fdwi)
fbval = dname + 'P64_F01.bval'
fbvec = dname + 'P64_F01.bvec'
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
fmask = dname + 'mask_extern.nii'
mask_vol, mask_affine = load_nifti(fmask)
sh_order = 8
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
def simple_viewer(streamlines, vol, affine):
from dipy.viz import actor, window
renderer = window.Renderer()
renderer.add(actor.line(streamlines))
renderer.add(actor.slicer(vol, affine))
window.show(renderer)
dname = "/Users/ghfc/Desktop/Celine/brainhack/data/"
fdwi = dname + "2dseq_conv_32.nii.gz"
data, affine = load_nifti(fdwi)
fbval = dname + "P64_F01.bval"
fbvec = dname + "P64_F01.bvec"
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
fmask = dname + "mask_extern.nii"
mask_vol, mask_affine = load_nifti(fmask)
sh_order = 8
if data.shape[-1] < 15:
raise ValueError(
def track(dname, fdwi, fbval, fbvec, fmask=None, seed_density = 1, show=False):
data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=50)
if fmask is None:
from dipy.segment.mask import median_otsu
b0_mask, mask = median_otsu(data) # TODO: check parameters to improve the mask
else:
mask, mask_affine = load_nifti(fmask)
mask = np.squeeze(mask) #fix mask dimensions
# compute DTI model
from dipy.reconst.dti import TensorModel
tenmodel = TensorModel(gtab)#, fit_method='OLS') #, min_signal=5000)
# fit the dti model
tenfit = tenmodel.fit(data, mask=mask)
# save fa
ffa = dname + 'tensor_fa.nii.gz'
fa_img = nib.Nifti1Image(tenfit.fa.astype(np.float32), affine)
nib.save(fa_img, ffa)
sh_order = 8 #TODO: check what that does
if data.shape[-1] < 15:
raise ValueError('You need at least 15 unique DWI volumes to '
'compute fiber ODFs. You currently have: {0}'
' DWI volumes.'.format(data.shape[-1]))
elif data.shape[-1] < 30:
sh_order = 6
# compute the response equation ?
from dipy.reconst.csdeconv import auto_response
response, ratio = auto_response(gtab, data)
response = list(response)
peaks_sphere = get_sphere('symmetric362')
#TODO: check what that does
peaks_csd = peaks_from_model(model=tenmodel,
data=data,
sphere=peaks_sphere,
relative_peak_threshold=.5, #.5
min_separation_angle=25,
mask=mask,
return_sh=True,
sh_order=sh_order,
normalize_peaks=True,
parallel=False)
peaks_csd.affine = affine
fpeaks = dname + 'peaks.npz'
save_peaks(fpeaks, peaks_csd)
from dipy.io.trackvis import save_trk
from dipy.tracking import utils
from dipy.tracking.local import (ThresholdTissueClassifier,
LocalTracking)
stopping_thr = 0.25 #0.25
pam = load_peaks(fpeaks)
#ffa = dname + 'tensor_fa_nomask.nii.gz'
fa, fa_affine = load_nifti(ffa)
classifier = ThresholdTissueClassifier(fa,
stopping_thr)
# seeds
seed_mask = fa > 0.4 #0.4 #TODO: check this parameter
seeds = utils.seeds_from_mask(
seed_mask,
density=seed_density,
affine=affine)
# tractography, if affine then in world coordinates
streamlines = LocalTracking(pam, classifier,
seeds, affine=affine, step_size=.5)
# Compute streamlines and store as a list.
streamlines = list(streamlines)
ftractogram = dname + 'tractogram.trk'
#save .trk
save_trk_old_style(ftractogram, streamlines, affine, fa.shape)
if show:
#render
show_results(data,streamlines, fa, fa_affine)