def update(self):
enable = self.calib()
self.seq_tr_num.Enable(enable)
self.calib_image_picker.Enable(enable)
self.calib_gain_num.Enable(enable)
self.coil_image_picker.checkbox.Enable(enable)
if self.analysis.white_paper():
self.calib_mode_ch.SetSelection(1)
self.calib_mode_ch.Enable(enable and not self.analysis.white_paper())
self.ref_tissue_type_ch.Enable(enable and self.refregion())
if self.ref_tissue_type() == 3:
# Ref tissue = None - enforce mask
self.ref_tissue_mask_picker.checkbox.Enable(False)
self.ref_tissue_mask_picker.checkbox.SetValue(enable and self.refregion())
self.ref_tissue_mask_picker.Enable(enable and self.refregion())
else:
self.ref_tissue_mask_picker.checkbox.Enable(enable and self.refregion())
self.ref_tissue_mask_picker.Enable(enable and self.refregion() and self.ref_tissue_mask_picker.checkbox.IsChecked())
self.coil_image_picker.checkbox.Enable(enable and self.refregion())
self.coil_image_picker.Enable(enable and self.refregion() and self.coil_image_picker.checkbox.IsChecked())
self.seq_te_num.Enable(enable and self.refregion())
self.blood_t2_num.Enable(enable and self.refregion())
self.ref_t1_num.Enable(enable and self.refregion())
self.ref_t2_num.Enable(enable and self.refregion())
TabPage.update(self)
def update(self):
mode = self.struc_ch.GetSelection()
self.fsl_anat_picker.Enable(mode == self.EXISTING_FSLANAT)
self.struc_image_picker.Enable(mode in (self.NEW_FSLANAT,
self.INDEP_STRUC))
self.brain_image_picker.checkbox.Enable(mode == self.INDEP_STRUC)
self.brain_image_picker.Enable(
mode == self.INDEP_STRUC
and self.brain_image_picker.checkbox.IsChecked())
TabPage.update(self)
def update(self):
self.distcorr_ch.Enable(self.distcorr())
cal = self.distcorr() and not self.distcorr_fmap()
self.calib_picker.Enable(cal)
fmap = self.distcorr() and self.distcorr_fmap()
self.fmap_picker.Enable(fmap)
self.fmap_mag_picker.Enable(fmap)
self.fmap_be_picker.Enable(fmap)
self.pedir_ch.Enable(self.distcorr())
self.echosp_num.Enable(self.distcorr())
TabPage.update(self)
def __init__(self, parent, idx, n):
TabPage.__init__(self,
parent,
"Distortion Correction",
idx,
n,
name="distcorr")
self.distcorr_choices = ["Fieldmap", "Calibration image"]
self.section("Distortion Correction")
# Calibration image options
self.distcorr_cb = wx.CheckBox(self,
label="Apply distortion correction")
self.distcorr_cb.Bind(wx.EVT_CHECKBOX, self._changed)
self.distcorr_ch = wx.Choice(self, choices=self.distcorr_choices[:1])
self.distcorr_ch.SetSelection(self.FIELDMAP)
self.distcorr_ch.Bind(wx.EVT_CHOICE, self._changed)
self.pack("", self.distcorr_cb, self.distcorr_ch, enable=False)
# Calib image options
self.section("Calibration Image Mode")
self.calib_picker = self.file_picker(
"Phase-encode-reversed calibration image")
# Fieldmap options
self.section("Fieldmap Mode")
self.fmap_picker = self.file_picker("Fieldmap image (in rad/s)")
self.fmap_mag_picker = self.file_picker("Fieldmap magnitude image")
self.fmap_be_picker = self.file_picker(
"Brain-extracted magnitude image", optional=True)
# General options
self.section("General")
self.echosp_num = self.number("Effective EPI echo spacing",
minval=0,
maxval=10)
self.pedir_ch = self.choice("Phase encoding direction",
choices=["x", "y", "z", "-x", "-y", "-z"])
self.sizer.AddGrowableCol(1, 1)
#sizer.AddGrowableRow(5, 1)
self.SetSizer(self.sizer)
self.next_prev()
def update(self):
self.ti_list.set_size(self.ntis())
self.bolus_dur_list.set_size(self.ntis())
self.time_per_slice_num.Enable(self.readout_2d())
self.multiband_cb.Enable(self.readout_2d())
self.slices_per_band_spin.Enable(self.multiband()
and self.readout_2d())
self.slices_per_band_label.Enable(self.multiband()
and self.readout_2d())
self.bolus_dur_num.Enable(not self.bolus_dur_multi())
self.bolus_dur_list.Enable(self.bolus_dur_multi())
self.tc_ch.Enable(self.tc_pairs())
self.update_groups()
TabPage.update(self)
def __init__(self, parent, idx, n):
TabPage.__init__(self, parent, "Analysis", idx, n)
self.distcorr_choices = ["Fieldmap", "Calibration image"]
self.section("Basic analysis options")
self.outdir_picker = self.file_picker("Output Directory",
pick_dir=True)
self.mask_picker = self.file_picker("Brain Mask", optional=True)
self.wp_cb = self.checkbox(
"Analysis which conforms to 'White Paper' (Alsop et al 2014)",
handler=self.wp_changed)
self.section("Initial parameter values")
self.bat_num = self.number("Arterial Transit Time (s)",
minval=0,
maxval=2.5,
initial=1.3)
self.t1_num = self.number("T1 (s)", minval=0, maxval=3, initial=1.3)
self.t1b_num = self.number("T1b (s)", minval=0, maxval=3, initial=1.65)
self.ie_num = self.number("Inversion Efficiency",
minval=0,
maxval=1,
initial=0.85)
self.section("Analysis Options")
self.spatial_cb = self.checkbox(
"Adaptive spatial regularization on perfusion", initial=True)
self.infer_t1_cb = self.checkbox("Incorporate T1 value uncertainty")
self.macro_cb = self.checkbox("Include macro vascular component")
self.fixbolus_cb = self.checkbox("Fix label duration", initial=True)
self.pv_cb = self.checkbox("Partial Volume Correction")
self.mc_cb = self.checkbox("Motion Correction")
self.sizer.AddGrowableCol(1, 1)
#sizer.AddGrowableRow(5, 1)
self.SetSizer(self.sizer)
self.next_prev()
def __init__(self, parent, idx, n):
TabPage.__init__(self, parent, "Structure", idx, n, name="structure")
self.section("Structure")
self.struc_ch = wx.Choice(self,
choices=[
"Existing FSL_ANAT output",
"Run FSL_ANAT on structural image",
"Independent structural data", "None"
])
self.struc_ch.SetSelection(self.NONE)
self.struc_ch.Bind(wx.EVT_CHOICE, self._changed)
self.struc_ch.span = 2
self.pack("Structural data from", self.struc_ch)
self.fsl_anat_picker = self.file_picker("Existing FSL_ANAT directory",
pick_dir=True)
self.struc_image_picker = self.file_picker("Structural Image")
self.brain_image_picker = self.file_picker("Brain image",
optional=True)
self.section("Registration")
self.transform_choices = [
"Use matrix", "Use warp image", "Use FSL_ANAT"
]
self.transform_cb = wx.CheckBox(self,
label="Transform to standard space")
self.transform_cb.Bind(wx.EVT_CHECKBOX, self._changed)
self.pack("", self.transform_cb, enable=False)
self.sizer.AddGrowableCol(2, 1)
self.SetSizer(self.sizer)
self.next_prev()
def __init__(self, parent, idx, n):
TabPage.__init__(self, parent, "Calibration", idx, n)
self.calib_cb = self.checkbox("Enable Calibration", bold=True, handler=self.calib_changed)
self.calib_image_picker = self.file_picker("Calibration Image")
self.seq_tr_num = self.number("Sequence TR (s)", minval=0, maxval=10, initial=6)
self.calib_gain_num = self.number("Calibration Gain", minval=0, maxval=5, initial=1)
self.calib_mode_ch = self.choice("Calibration mode", choices=["Reference Region", "Voxelwise"])
self.section("Reference tissue")
self.ref_tissue_type_ch = self.choice("Type", choices=["CSF", "WM", "GM", "None"],
handler=self.ref_tissue_type_changed)
self.ref_tissue_mask_picker = self.file_picker("Mask", optional=True)
self.ref_t1_num = self.number("Reference T1 (s)", minval=0, maxval=5, initial=4.3)
self.seq_te_num = self.number("Sequence TE (ms)", minval=0, maxval=30, initial=0)
self.ref_t2_num = self.number("Reference T2 (ms)", minval=0, maxval=1000, initial=750, step=10)
self.blood_t2_num = self.number("Blood T2 (ms)", minval=0, maxval=1000, initial=150, step=10)
self.coil_image_picker = self.file_picker("Coil Sensitivity Image", optional=True)
self.sizer.AddGrowableCol(2, 1)
self.SetSizer(self.sizer)
self.next_prev()
def update(self):
self.mask_picker.Enable(self.mask_picker.checkbox.IsChecked())
self.t1_num.Enable(not self.white_paper())
self.bat_num.Enable(not self.white_paper())
TabPage.update(self)
def __init__(self, parent, idx, n):
TabPage.__init__(self, parent, "Input Data", idx, n, name="input")
self.groups = ["PLDs", "Repeats", "Label/Control pairs"]
self.abbrevs = ["t", "r", "l"]
self.section("Data contents")
self.data_picker = self.file_picker("Input Image",
handler=self.set_default_dir)
self.ntis_int = self.integer("Number of PLDs",
minval=1,
maxval=100,
initial=1)
self.nrepeats_label = wx.StaticText(self, label="<Unknown>")
self.pack("Number of repeats", self.nrepeats_label)
self.section("Data order")
self.choice1 = wx.Choice(self, choices=self.groups)
self.choice1.SetSelection(2)
self.choice1.Bind(wx.EVT_CHOICE, self._changed)
self.choice2 = wx.Choice(self, choices=self.groups)
self.choice2.SetSelection(0)
self.choice2.Bind(wx.EVT_CHOICE, self._changed)
self.pack("Grouping order", self.choice1, self.choice2)
self.tc_ch = self.choice(
"Label/Control pairs",
choices=["Label then control", "Control then label"],
optional=True,
initial_on=True)
self.section("Acquisition parameters")
self.labelling_ch = self.choice("Labelling",
choices=["pASL", "cASL/pcASL"],
initial=1,
handler=self.labelling_changed)
self.bolus_dur_ch = wx.Choice(self, choices=["Constant", "Variable"])
self.bolus_dur_ch.SetSelection(0)
self.bolus_dur_ch.Bind(wx.EVT_CHOICE, self._changed)
self.bolus_dur_num = NumberChooser(self,
minval=0,
maxval=2.5,
step=0.1,
initial=1.8)
self.bolus_dur_num.span = 2
self.bolus_dur_num.spin.Bind(wx.EVT_SPINCTRL, self.bolus_dur_changed)
self.bolus_dur_num.slider.Bind(wx.EVT_SLIDER, self.bolus_dur_changed)
self.pack("Bolus duration (s)", self.bolus_dur_ch, self.bolus_dur_num)
self.bolus_dur_list = NumberList(self, self.ntis())
self.bolus_dur_list.span = 3
self.bolus_dur_list.Bind(wx.grid.EVT_GRID_CELL_CHANGED, self._changed)
self.pack("Bolus durations (s)", self.bolus_dur_list, enable=False)
self.ti_list = NumberList(self, self.ntis())
self.ti_list.span = 3
self.ti_list.Bind(wx.grid.EVT_GRID_CELL_CHANGED, self._changed)
self.pack("PLDs (s)", self.ti_list)
self.readout_ch = wx.Choice(
self, choices=["3D (eg GRASE)", "2D multi-slice (eg EPI)"])
self.readout_ch.SetSelection(0)
self.readout_ch.Bind(wx.EVT_CHOICE, self._changed)
self.time_per_slice_num = NumberChooser(self,
label="Time per slice (ms)",
minval=0,
maxval=50,
step=1,
initial=10)
self.time_per_slice_num.span = 2
self.pack("Readout", self.readout_ch, self.time_per_slice_num)
self.time_per_slice_num.Enable(False)
self.multiband_cb = wx.CheckBox(self, label="Multi-band")
self.multiband_cb.Bind(wx.EVT_CHECKBOX, self._changed)
self.slices_per_band_spin = wx.SpinCtrl(self,
min=1,
max=100,
initial=5)
self.slices_per_band_label = wx.StaticText(self,
label="slices per band")
self.pack("",
self.multiband_cb,
self.slices_per_band_spin,
self.slices_per_band_label,
enable=False)
self.multiband_cb.Enable(False)
self.sizer.AddGrowableCol(2, 1)
self.SetSizer(self.sizer)
self.next_prev()