Use QI mask instead of BET

spinicist · Nov 29, 2023 · 8ddeaec · 8ddeaec
1 parent f8cff8b
commit 8ddeaec
Showing 1 changed file with 57 additions and 59 deletions.
diff --git a/Python/qipype/workflows/mpm.py b/Python/qipype/workflows/mpm.py
@@ -1,12 +1,63 @@
 import numpy as np
 from nipype import Workflow, Node, MapNode, IdentityInterface
-from nipype.interfaces.fsl import maths, BET, MCFLIRT, ExtractROI, FLIRT, Merge, ApplyXFM, ImageMaths, BinaryMaths, ConvertXFM
+from nipype.interfaces.fsl import FLIRT, Merge, ApplyXFM, ImageMaths
 import nipype.interfaces.utility as util
 from qipype.fitting import MPMR2s, MTSat
 from qipype.commands import B1Minus
 from qipype.fsl import ApplyXfm4D
-from qipype.utils import Select
+from qipype.utils import Select, Mask
 
+def init_mpm_wf(me_params, mtsat_params):
+    inputnode = Node(IdentityInterface(fields=['PDw_file', 'T1w_file', 'MTw_file', 'B1_map']),
+                     name='inputnode')
+    outputnode = Node(IdentityInterface(fields=['PD_map', 'R1_map', 'R2s_map', 'mtsat_map', 'brain_mask']),
+                      name='outputnode')
+
+    wf = Workflow(name='Multi-Parametric-Mapping')
+
+    mask = Node(Mask(vol=0), name='mask')
+    wf.connect([(inputnode, mask, [('PDw_file', 'in_file')])])
+
+    pd0 = Node(Select(volumes=[0, ], out_file='pd0.nii.gz'), name='pd0')
+    t10 = Node(Select(volumes=[0, ], out_file='t10.nii.gz'), name='t10')
+    mt0 = Node(Select(volumes=[0, ], out_file='mt0.nii.gz'), name='mt0')
+    wf.connect([(inputnode, pd0, [('PDw_file', 'in_file')]),
+                (inputnode, t10, [('T1w_file', 'in_file')]),
+                (inputnode, mt0, [('MTw_file', 'in_file')])])
+
+    t1_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='t1_reg')
+    mt_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='mt_reg')
+    t1_apply = Node(ApplyXfm4D(single_matrix=True), name='t1_apply')
+    mt_apply = Node(ApplyXfm4D(single_matrix=True), name='mt_apply')
+    wf.connect([(t10, t1_reg, [('out_file', 'in_file')]),
+                (pd0, t1_reg, [('out_file', 'reference')]),
+                (inputnode, t1_apply, [('T1w_file', 'in_file')]),
+                (pd0, t1_apply, [('out_file', 'ref_vol')]),
+                (t1_reg, t1_apply, [('out_matrix_file', 'trans_file')]),
+                (mt0, mt_reg, [('out_file', 'in_file')]),
+                (pd0, mt_reg, [('out_file', 'reference')]),
+                (inputnode, mt_apply, [('MTw_file', 'in_file')]),
+                (pd0, mt_apply, [('out_file', 'ref_vol')]),
+                (mt_reg, mt_apply, [('out_matrix_file', 'trans_file')])])
+
+    mpm = Node(MPMR2s(sequence=me_params, verbose=True), name='MPM_R2s')
+    mtsat = Node(MTSat(sequence=mtsat_params, verbose=True), name='MPM_MTSat')
+
+    wf.connect([(inputnode, mpm, [('PDw_file', 'PDw_file')]),
+                (t1_apply, mpm, [('out_file', 'T1w_file')]),
+                (mt_apply, mpm, [('out_file', 'MTw_file')]),
+                (mask, mpm, [('out_file', 'mask_file')]),
+                (mpm, mtsat, [('S0_PDw_map', 'PDw_file'),
+                              ('S0_T1w_map', 'T1w_file'),
+                              ('S0_MTw_map', 'MTw_file')]),
+                (inputnode, mtsat, [('B1_map', 'B1_map')]),
+                (mask, mtsat, [('out_file', 'mask_file')]),
+                (mpm, outputnode, [('R2s_map', 'R2s_map')]),
+                (mtsat, outputnode, [('PD_map', 'PD_map'),
+                                     ('R1_map', 'R1_map'),
+                                     ('delta_map', 'mtsat_map')]),
+                (mask, outputnode, [('out_file', 'brain_mask')])])
+    return wf
 
 def init_mpm_b1_wf(me_params, mtsat_params):
     inputnode = Node(IdentityInterface(fields=['PDw_file', 'T1w_file', 'MTw_file',
@@ -18,8 +69,8 @@ def init_mpm_b1_wf(me_params, mtsat_params):
 
     wf = Workflow(name='Multi-Parametric-Mapping')
 
-    bet = Node(BET(mask=True, no_output=True), name='brain_mask')
-    wf.connect([(inputnode, bet, [('T1w_file', 'in_file')])])
+    mask = Node(Mask(vol=0), name='mask')
+    wf.connect([(inputnode, mask, [('PDw_file', 'in_file')])])
 
     PD_B1minus = Node(B1Minus(), name='PD_B1minus')
     t1_B1minus = Node(B1Minus(), name='t1_B1minus')
@@ -82,67 +133,14 @@ def init_mpm_b1_wf(me_params, mtsat_params):
     wf.connect([(pd_cal, mpm, [('out_file', 'PDw_file')]),
                 (t1_apply, mpm, [('out_file', 'T1w_file')]),
                 (mt_apply, mpm, [('out_file', 'MTw_file')]),
-                (bet, mpm, [('mask_file', 'mask_file')]),
+                (mask, mpm, [('out_file', 'mask_file')]),
                 (mpm, mtsat, [('S0_PDw_map', 'PDw_file'),
                               ('S0_T1w_map', 'T1w_file'),
                               ('S0_MTw_map', 'MTw_file')]),
                 (inputnode, mtsat, [('B1_map', 'B1_map')]),
-                (bet, mtsat, [('mask_file', 'mask_file')]),
+                (mask, mtsat, [('out_file', 'mask_file')]),
                 (mpm, outputnode, [('R2s_map', 'R2s_map')]),
                 (mtsat, outputnode, [('PD_map', 'PD_map'),
                                      ('R1_map', 'R1_map'),
                                      ('delta_map', 'mtsat_map')])])
     return wf
-
-
-def init_mpm_wf(me_params, mtsat_params):
-    inputnode = Node(IdentityInterface(fields=['PDw_file', 'T1w_file', 'MTw_file', 'B1_map']),
-                     name='inputnode')
-    outputnode = Node(IdentityInterface(fields=['PD_map', 'R1_map', 'R2s_map', 'mtsat_map', 'brain_mask']),
-                      name='outputnode')
-
-    wf = Workflow(name='Multi-Parametric-Mapping')
-
-    bet = Node(BET(mask=True, no_output=True), name='brain_mask')
-    wf.connect([(inputnode, bet, [('T1w_file', 'in_file')])])
-
-    pd0 = Node(Select(volumes=[0, ], out_file='pd0.nii.gz'), name='pd0')
-    t10 = Node(Select(volumes=[0, ], out_file='t10.nii.gz'), name='t10')
-    mt0 = Node(Select(volumes=[0, ], out_file='mt0.nii.gz'), name='mt0')
-    wf.connect([(inputnode, pd0, [('PDw_file', 'in_file')]),
-                (inputnode, t10, [('T1w_file', 'in_file')]),
-                (inputnode, mt0, [('MTw_file', 'in_file')])])
-
-    t1_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='t1_reg')
-    mt_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='mt_reg')
-    t1_apply = Node(ApplyXfm4D(single_matrix=True), name='t1_apply')
-    mt_apply = Node(ApplyXfm4D(single_matrix=True), name='mt_apply')
-    wf.connect([(t10, t1_reg, [('out_file', 'in_file')]),
-                (pd0, t1_reg, [('out_file', 'reference')]),
-                (inputnode, t1_apply, [('T1w_file', 'in_file')]),
-                (pd0, t1_apply, [('out_file', 'ref_vol')]),
-                (t1_reg, t1_apply, [('out_matrix_file', 'trans_file')]),
-                (mt0, mt_reg, [('out_file', 'in_file')]),
-                (pd0, mt_reg, [('out_file', 'reference')]),
-                (inputnode, mt_apply, [('MTw_file', 'in_file')]),
-                (pd0, mt_apply, [('out_file', 'ref_vol')]),
-                (mt_reg, mt_apply, [('out_matrix_file', 'trans_file')])])
-
-    mpm = Node(MPMR2s(sequence=me_params, verbose=True), name='MPM_R2s')
-    mtsat = Node(MTSat(sequence=mtsat_params, verbose=True), name='MPM_MTSat')
-
-    wf.connect([(inputnode, mpm, [('PDw_file', 'PDw_file')]),
-                (t1_apply, mpm, [('out_file', 'T1w_file')]),
-                (mt_apply, mpm, [('out_file', 'MTw_file')]),
-                (bet, mpm, [('mask_file', 'mask_file')]),
-                (mpm, mtsat, [('S0_PDw_map', 'PDw_file'),
-                              ('S0_T1w_map', 'T1w_file'),
-                              ('S0_MTw_map', 'MTw_file')]),
-                (inputnode, mtsat, [('B1_map', 'B1_map')]),
-                (bet, mtsat, [('mask_file', 'mask_file')]),
-                (mpm, outputnode, [('R2s_map', 'R2s_map')]),
-                (mtsat, outputnode, [('PD_map', 'PD_map'),
-                                     ('R1_map', 'R1_map'),
-                                     ('delta_map', 'mtsat_map')]),
-                (bet, outputnode, [('mask_file', 'brain_mask')])])
-    return wf