class FslAtlasWidget(QpWidget):
"""
Widget for browsing and loading FSL atlases
"""
def __init__(self, **kwargs):
super(FslAtlasWidget,
self).__init__(name="Atlases",
icon="fsl.png",
desc="Browse and display FSL atlases",
group="FSL",
**kwargs)
self._registry = AtlasRegistry()
def init_ui(self):
vbox = QtGui.QVBoxLayout()
vbox.setSpacing(1)
self.setLayout(vbox)
vbox.addWidget(TitleWidget(self))
vbox.addWidget(Citation(*CITATIONS["fsl"]))
self.atlas_list = AtlasListWidget(self, self._registry)
vbox.addWidget(self.atlas_list)
self.atlas_desc = AtlasDescription(self, self._registry)
vbox.addWidget(self.atlas_desc)
self.atlas_list.sig_selected.connect(self.atlas_desc.set_atlas)
fsldir = FslDirWidget()
vbox.addWidget(fsldir)
# This needs to be done after creating the FslDirWidget because otherwise we may not
# have picked up a previously saved FSLDIR setting and the atlas list will be empty
self._registry.rescanAtlases()
self.atlas_list.init_list()
def get_tissrefmask(wsp):
"""
Calculate a calibration reference mask for a particular known tissue type
"""
page = wsp.report.page("auto_calib_mask")
page.heading("Calibration reference region")
page.text("Reference region was automatically generated for tissue type: %s" % wsp.tissref.upper())
page.heading("Partial volume map for %s tissue (from structural segmentation)" % wsp.tissref.upper(), level=1)
wsp.calibration.refpve = getattr(wsp.structural, "%s_pv" % wsp.tissref.lower())
page.image("refpve", LightboxImage(wsp.calibration.refpve, bgimage=wsp.structural.brain))
if wsp.tissref == "csf" and not wsp.csfmaskingoff:
wsp.log.write(" - Doing automatic ventricle selection using standard atlas\n")
# By deafult now we do FNRIT transformation of ventricle mask
# FIXME disabled as not being used in ASL_CALIB at present
#wsp.calibration.struc2stdfnirt = wsp.ifnone("stdmaskfnirt", True)
# Select ventricles based on standard space atlas
page.heading("Automatic ventricle selection", level=1)
page.text("Standard space ventricles mask (from Harvard-Oxford atlas) eroded by 1 pixel")
atlases = AtlasRegistry()
atlases.rescanAtlases()
atlas = atlases.loadAtlas("harvardoxford-subcortical", loadSummary=False, resolution=2)
ventricles = ((atlas.data[..., 2] + atlas.data[..., 13]) > 0.1).astype(np.int)
wsp.calibration.ventricles = Image(scipy.ndimage.binary_erosion(ventricles, structure=np.ones([3, 3, 3]), border_value=1).astype(np.int), header=atlas.header)
std_img = Image(os.path.join(os.environ["FSLDIR"], "data", "standard", 'MNI152_T1_2mm_brain'))
page.image("ventricles_std", LightboxImage(wsp.calibration.ventricles, bgimage=std_img))
page.heading("Structural space ventricles mask", level=1)
# FIXME nearest neighbour interpolation?
wsp.calibration.ventricles_struc = reg.change_space(wsp, wsp.calibration.ventricles, "struc")
page.text("This is the above image transformed into structural space. The transformation was obtained by registering the structural image to the standard brain image")
page.image("ventricles_struc", LightboxImage(wsp.calibration.ventricles_struc, bgimage=wsp.structural.brain))
wsp.log.write(" - Masking FAST output with standard space derived ventricle mask\n")
wsp.calibration.refpve_pre_mask = wsp.calibration.refpve
refpve_data = np.copy(wsp.calibration.refpve.data)
refpve_data[wsp.calibration.ventricles_struc.data == 0] = 0
wsp.calibration.refpve = Image(refpve_data, header=wsp.calibration.refpve.header)
wsp.calibration.refpve_post = wsp.calibration.refpve
page.heading("Structural space ventricles PVE", level=1)
page.text("This is the CSF partial volume masked by the ventricles mask. It should select only the ventricles from the original partial volume image.")
page.image("refpve_post", LightboxImage(wsp.calibration.refpve, bgimage=wsp.structural.brain))
wsp.log.write(" - Transforming tissue reference mask into ASL space\n")
# FIXME calibration image may not be in ASL space! Oxford_asl does not handle this currently
wsp.calibration.refpve_calib = reg.change_space(wsp, wsp.calibration.refpve, "native")
#wsp.calibration.refpve_calib.data[wsp.calibration.refpve_calib.data < 0.001] = 0 # Better for display
page.heading("Reference region in ASL space", level=1)
page.text("Partial volume map")
page.image("refpve_calib", LightboxImage(wsp.calibration.refpve_calib, bgimage=wsp.calibration.calib_img))
# Threshold reference mask conservatively to select only reference tissue
wsp.log.write(" - Thresholding reference mask\n")
wsp.calibration.refmask = Image((wsp.calibration.refpve_calib.data > 0.9).astype(np.int), header=wsp.calibration.refpve_calib.header)
page.text("Reference Mask (thresholded at 0.9")
page.image("refmask", LightboxImage(wsp.calibration.refmask, bgimage=wsp.calibration.calib_img))
def __init__(self, **kwargs):
super(FslAtlasWidget,
self).__init__(name="Atlases",
icon="fsl.png",
desc="Browse and display FSL atlases",
group="FSL",
**kwargs)
self._registry = AtlasRegistry()
def __init__(self, ivm):
StructureModel.__init__(self, ivm, "FSL MNI standard data")
from fsl.data.atlases import AtlasRegistry
self._registry = AtlasRegistry()
self._registry.rescanAtlases()
atlas_names = []
self._atlases = {}
for atlas in sorted(self._registry.listAtlases(),
key=lambda x: x.name):
for prefix in self.ATLAS_PREFIXES:
if atlas.name.startswith(prefix):
for pixdim in atlas.pixdims:
name = atlas.name + " %.2gx%.2gx%.2g mm" % pixdim
self._atlases[name] = (atlas, pixdim)
class FslStdStructureModel(PartialVolumeStructureModel):
"""
Structural model using standard FSL structural data
FIXME not functional at present - not clear that FSL supplies relevant
segmentation data out of the box!
"""
NAME = "fsl"
ATLAS_PREFIXES = [
"MNI",
]
def __init__(self, ivm):
StructureModel.__init__(self, ivm, "FSL MNI standard data")
from fsl.data.atlases import AtlasRegistry
self._registry = AtlasRegistry()
self._registry.rescanAtlases()
atlas_names = []
self._atlases = {}
for atlas in sorted(self._registry.listAtlases(),
key=lambda x: x.name):
for prefix in self.ATLAS_PREFIXES:
if atlas.name.startswith(prefix):
for pixdim in atlas.pixdims:
name = atlas.name + " %.2gx%.2gx%.2g mm" % pixdim
self._atlases[name] = (atlas, pixdim)
@property
def structures(self):
atlas, pixdims = self._atlases[self.options["atlas"]]
structures = []
for label in atlas.labels:
structures.append(Parameter(label.name, label.name))
return structures
@property
def structure_maps(self):
atlas, pixdims = self._atlases[self.options["atlas"]]
structure_maps = {}
atlas_map = self._registry.loadAtlas(atlas.atlasID,
loadSummary=False,
resolution=pixdims[0])
for idx, label in enumerate(atlas.labels):
structure_maps[label.name] = fslimage_to_qpdata(atlas_map,
vol=idx,
name=label.name)
return structure_maps