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dPys
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[MAINT] Re-run circle
1 parent acc9721 commit 2a4695b

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6 files changed

+114
-72
lines changed

6 files changed

+114
-72
lines changed

‎pynets/core/interfaces.py‎

Lines changed: 44 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -574,6 +574,7 @@ def _run_interface(self, runtime):
574574
template_tmp_path,
575575
self.inputs.simple,
576576
)
577+
time.sleep(0.5)
577578

578579
if self.inputs.mask:
579580
out_name_mask = fname_presuffix(
@@ -1143,11 +1144,12 @@ class RegisterDWI(SimpleInterface):
11431144

11441145
def _run_interface(self, runtime):
11451146
import gc
1147+
import time
11461148
import glob
11471149
import os.path as op
11481150
from pynets.registration import register
1149-
from pynets.registration import reg_utils as regutils
11501151
from nipype.utils.filemanip import fname_presuffix, copyfile
1152+
from pynets.registration.reg_utils import check_orient_and_dims
11511153

11521154
fa_tmp_path = fname_presuffix(
11531155
self.inputs.fa_path, suffix="_tmp", newpath=runtime.cwd
@@ -1205,6 +1207,9 @@ def _run_interface(self, runtime):
12051207
mask_tmp_path,
12061208
copy=True,
12071209
use_hardlink=False)
1210+
mask_tmp_path = check_orient_and_dims(
1211+
mask_tmp_path, runtime.cwd, self.inputs.vox_size
1212+
)
12081213
else:
12091214
mask_tmp_path = None
12101215

@@ -1218,6 +1223,9 @@ def _run_interface(self, runtime):
12181223
gm_mask,
12191224
copy=True,
12201225
use_hardlink=False)
1226+
gm_mask = check_orient_and_dims(
1227+
gm_mask, runtime.cwd, self.inputs.vox_size
1228+
)
12211229
else:
12221230
gm_mask = None
12231231

@@ -1231,6 +1239,9 @@ def _run_interface(self, runtime):
12311239
wm_mask,
12321240
copy=True,
12331241
use_hardlink=False)
1242+
wm_mask = check_orient_and_dims(
1243+
wm_mask, runtime.cwd, self.inputs.vox_size
1244+
)
12341245
else:
12351246
wm_mask = None
12361247

@@ -1245,6 +1256,9 @@ def _run_interface(self, runtime):
12451256
csf_mask,
12461257
copy=True,
12471258
use_hardlink=False)
1259+
csf_mask = check_orient_and_dims(
1260+
csf_mask, runtime.cwd, self.inputs.vox_size
1261+
)
12481262
else:
12491263
csf_mask = None
12501264

@@ -1270,9 +1284,11 @@ def _run_interface(self, runtime):
12701284

12711285
# Generate T1w brain mask
12721286
reg.gen_mask(mask_tmp_path)
1287+
time.sleep(0.5)
12731288

12741289
# Perform anatomical segmentation
12751290
reg.gen_tissue(wm_mask, gm_mask, csf_mask, self.inputs.overwrite)
1291+
time.sleep(0.5)
12761292

12771293
# Align t1w to mni template
12781294
# from joblib import Memory
@@ -1284,17 +1300,20 @@ def _run_interface(self, runtime):
12841300
# t1w2mni_align = memory.cache(reg.t1w2mni_align)
12851301
# t1w2mni_align()
12861302
reg.t1w2mni_align()
1303+
time.sleep(0.5)
12871304

12881305
if (self.inputs.overwrite is True) or (
12891306
op.isfile(reg.t1w2dwi) is False):
12901307
# Align t1w to dwi
12911308
reg.t1w2dwi_align()
1309+
time.sleep(0.5)
12921310

12931311
if (self.inputs.overwrite is True) or (
12941312
op.isfile(reg.wm_gm_int_in_dwi) is False
12951313
):
12961314
# Align tissue
12971315
reg.tissue2dwi_align()
1316+
time.sleep(0.5)
12981317

12991318
self._results["wm_in_dwi"] = reg.wm_in_dwi
13001319
self._results["gm_in_dwi"] = reg.gm_in_dwi
@@ -1389,6 +1408,7 @@ class RegisterAtlasDWI(SimpleInterface):
13891408

13901409
def _run_interface(self, runtime):
13911410
import gc
1411+
import time
13921412
import os
13931413
from pynets.registration import reg_utils as regutils
13941414
from pynets.core.nodemaker import \
@@ -1641,6 +1661,7 @@ def _run_interface(self, runtime):
16411661
template_tmp_path,
16421662
self.inputs.simple,
16431663
)
1664+
time.sleep(0.5)
16441665
os.remove(waymask_tmp_path)
16451666
else:
16461667
waymask_in_dwi = None
@@ -1743,6 +1764,7 @@ class RegisterROIDWI(SimpleInterface):
17431764
def _run_interface(self, runtime):
17441765
import gc
17451766
import os
1767+
import time
17461768
from pynets.registration import reg_utils as regutils
17471769
from nipype.utils.filemanip import fname_presuffix, copyfile
17481770
import pkg_resources
@@ -1856,6 +1878,7 @@ def _run_interface(self, runtime):
18561878
template_tmp_path,
18571879
self.inputs.simple,
18581880
)
1881+
time.sleep(0.5)
18591882
else:
18601883
roi_in_dwi = None
18611884

@@ -1914,10 +1937,11 @@ class RegisterFunc(SimpleInterface):
19141937
def _run_interface(self, runtime):
19151938
import gc
19161939
import glob
1940+
import time
19171941
import os.path as op
19181942
from pynets.registration import register
1919-
from pynets.registration import reg_utils as regutils
19201943
from nipype.utils.filemanip import fname_presuffix, copyfile
1944+
from pynets.registration.reg_utils import check_orient_and_dims
19211945

19221946
anat_mask_existing = [
19231947
i
@@ -1949,6 +1973,9 @@ def _run_interface(self, runtime):
19491973
mask_tmp_path,
19501974
copy=True,
19511975
use_hardlink=False)
1976+
mask_tmp_path = check_orient_and_dims(
1977+
mask_tmp_path, runtime.cwd, self.inputs.vox_size
1978+
)
19521979
else:
19531980
mask_tmp_path = None
19541981

@@ -1963,6 +1990,9 @@ def _run_interface(self, runtime):
19631990
gm_mask,
19641991
copy=True,
19651992
use_hardlink=False)
1993+
gm_mask = check_orient_and_dims(
1994+
gm_mask, runtime.cwd, self.inputs.vox_size
1995+
)
19661996
else:
19671997
gm_mask = None
19681998

@@ -1977,6 +2007,9 @@ def _run_interface(self, runtime):
19772007
wm_mask,
19782008
copy=True,
19792009
use_hardlink=False)
2010+
wm_mask = check_orient_and_dims(
2011+
wm_mask, runtime.cwd, self.inputs.vox_size
2012+
)
19802013
else:
19812014
wm_mask = None
19822015

@@ -1999,9 +2032,11 @@ def _run_interface(self, runtime):
19992032

20002033
# Generate T1w brain mask
20012034
reg.gen_mask(mask_tmp_path)
2035+
time.sleep(0.5)
20022036

20032037
# Perform anatomical segmentation
20042038
reg.gen_tissue(wm_mask, gm_mask, self.inputs.overwrite)
2039+
time.sleep(0.5)
20052040

20062041
# Align t1w to mni template
20072042
# from joblib import Memory
@@ -2013,6 +2048,7 @@ def _run_interface(self, runtime):
20132048
# t1w2mni_align = memory.cache(reg.t1w2mni_align)
20142049
# t1w2mni_align()
20152050
reg.t1w2mni_align()
2051+
time.sleep(0.5)
20162052

20172053
self._results["reg_fmri_complete"] = True
20182054
self._results["basedir_path"] = runtime.cwd
@@ -2059,6 +2095,7 @@ def _run_interface(self, runtime):
20592095
import gc
20602096
import os
20612097
import pkg_resources
2098+
import time
20622099
from pynets.core.utils import prune_suffices
20632100
from pynets.registration import reg_utils as regutils
20642101
from nipype.utils.filemanip import fname_presuffix, copyfile
@@ -2150,6 +2187,7 @@ def _run_interface(self, runtime):
21502187
t1w2mni_warp_tmp_path,
21512188
self.inputs.simple
21522189
)
2190+
time.sleep(0.5)
21532191

21542192
out_dir = f"{self.inputs.dir_path}/t1w_clustered_parcellations/"
21552193
os.makedirs(out_dir, exist_ok=True)
@@ -2220,6 +2258,7 @@ class RegisterAtlasFunc(SimpleInterface):
22202258
def _run_interface(self, runtime):
22212259
import gc
22222260
import os
2261+
import time
22232262
import glob
22242263
from pynets.registration import reg_utils as regutils
22252264
from pynets.core.nodemaker import \
@@ -2359,6 +2398,7 @@ def _run_interface(self, runtime):
23592398
aligned_atlas_gm,
23602399
self.inputs.simple,
23612400
)
2401+
time.sleep(0.5)
23622402

23632403
# Correct coords and labels
23642404
[aligned_atlas_gm, coords, labels] = \
@@ -2451,6 +2491,7 @@ class RegisterROIEPI(SimpleInterface):
24512491
def _run_interface(self, runtime):
24522492
import gc
24532493
import os
2494+
import time
24542495
from pynets.registration import reg_utils as regutils
24552496
from nipype.utils.filemanip import fname_presuffix, copyfile
24562497
import pkg_resources
@@ -2520,6 +2561,7 @@ def _run_interface(self, runtime):
25202561
template_tmp_path,
25212562
self.inputs.simple,
25222563
)
2564+
time.sleep(0.5)
25232565
else:
25242566
roi_in_t1w = None
25252567

‎pynets/dmri/track.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -520,7 +520,7 @@ def run_tracking(step_curv_combinations, atlas_data_wm_gm_int, recon_path,
520520
from nipype.utils.filemanip import copyfile, fname_presuffix
521521

522522
B0_mask_tmp_path = fname_presuffix(
523-
B0_mask,
523+
B0_mask, suffix=f"_{step_curv_combinations}",
524524
newpath=cache_dir
525525
)
526526
copyfile(

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