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chrisgorgochrisgorgo
authored
Merge pull request #35 from ntraut/master
skip subject only if last freesurfer output is present
2 parents b3220a0 + 1152a23 commit 119a738

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+25
-21
lines changed

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+25
-21
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‎run.py‎

Lines changed: 25 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -111,7 +111,7 @@ def run(command, env={}, ignore_errors=False):
111111
if glob(os.path.join(args.bids_dir, "sub-*", "ses-*")):
112112
subjects = [subject_dir.split("-")[-1] for subject_dir in subject_dirs]
113113
for subject_label in subjects:
114-
session_dirs = glob(os.path.join(args.bids_dir,"sub-%s"%subject_label,"ses-*"))
114+
session_dirs = glob(os.path.join(args.bids_dir, "sub-%s"%subject_label, "ses-*"))
115115
sessions = [os.path.split(dr)[-1].split("-")[-1] for dr in session_dirs]
116116
n_valid_sessions = 0
117117
for session_label in sessions:
@@ -161,36 +161,36 @@ def run(command, env={}, ignore_errors=False):
161161
for subject_label in subjects_to_analyze:
162162
if glob(os.path.join(args.bids_dir, "sub-%s"%subject_label, "ses-*")):
163163
T1s = glob(os.path.join(args.bids_dir,
164-
"sub-%s"%subject_label,
165-
"ses-*",
166-
"anat",
167-
"%s_T1w.nii*"%acq_tpl))
164+
"sub-%s"%subject_label,
165+
"ses-*",
166+
"anat",
167+
"%s_T1w.nii*"%acq_tpl))
168168
sessions = set([os.path.normpath(t1).split(os.sep)[-3].split("-")[-1] for t1 in T1s])
169169
if args.session_label:
170170
sessions = sessions.intersection(args.session_label)
171171

172172
if len(sessions) > 0 and longitudinal_study == True:
173173
timepoints = ["sub-%s_ses-%s"%(subject_label, session_label) for session_label in sessions]
174-
if ('cross-sectional' in args.steps):
174+
if 'cross-sectional' in args.steps:
175175
# Running each session separately, prior to doing longitudinal pipeline
176176
for session_label in sessions:
177177
T1s = glob(os.path.join(args.bids_dir,
178-
"sub-%s"%subject_label,
179-
"ses-%s"%session_label,
180-
"anat",
181-
"%s_T1w.nii*"%acq_tpl))
178+
"sub-%s"%subject_label,
179+
"ses-%s"%session_label,
180+
"anat",
181+
"%s_T1w.nii*"%acq_tpl))
182182
input_args = ""
183183
for T1 in T1s:
184-
if (round(max(nibabel.load(T1).header.get_zooms()),1) < 1.0 and args.hires_mode == "auto") or args.hires_mode == "enable":
184+
if (round(max(nibabel.load(T1).header.get_zooms()), 1) < 1.0 and args.hires_mode == "auto") or args.hires_mode == "enable":
185185
input_args += " -hires"
186186
input_args += " -i %s"%T1
187187

188188
T2s = glob(os.path.join(args.bids_dir, "sub-%s"%subject_label,
189189
"ses-%s"%session_label, "anat",
190190
"*%s_T2w.nii*"%acq_t2))
191191
FLAIRs = glob(os.path.join(args.bids_dir, "sub-%s"%subject_label,
192-
"ses-%s"%session_label, "anat",
193-
"*%s_FLAIR.nii*"%acq_t2))
192+
"ses-%s"%session_label, "anat",
193+
"*%s_FLAIR.nii*"%acq_t2))
194194
if args.refine_pial == "T2":
195195
for T2 in T2s:
196196
if max(nibabel.load(T2).header.get_zooms()) < 1.2:
@@ -219,7 +219,7 @@ def run(command, env={}, ignore_errors=False):
219219
print("DELETING OUTPUT SUBJECT DIR AND RE-RUNNING COMMAND:")
220220
print(cmd)
221221
run(cmd)
222-
elif os.path.isfile(os.path.join(output_dir, fsid, "mri/aseg.mgz")):
222+
elif os.path.isfile(os.path.join(output_dir, fsid, "label/BA_exvivo.thresh.ctab")):
223223
print("SUBJECT ALREADY SEGMENTED, SKIPPING")
224224
elif os.path.exists(os.path.join(output_dir, fsid)):
225225
print("SUBJECT DIR ALREADY EXISTS (without IsRunning.lh+rh), RUNNING COMMAND:")
@@ -228,8 +228,8 @@ def run(command, env={}, ignore_errors=False):
228228
else:
229229
print(cmd)
230230
run(cmd)
231-
232-
if ('template' in args.steps):
231+
232+
if 'template' in args.steps:
233233
# creating a subject specific template
234234
input_args = " ".join(["-tp %s"%tp for tp in timepoints])
235235
fsid = "sub-%s"%subject_label
@@ -240,12 +240,12 @@ def run(command, env={}, ignore_errors=False):
240240
stages,
241241
args.n_cpus)
242242

243-
if os.path.isfile(os.path.join(output_dir, fsid,"scripts/IsRunning.lh+rh")):
243+
if os.path.isfile(os.path.join(output_dir, fsid, "scripts/IsRunning.lh+rh")):
244244
rmtree(os.path.join(output_dir, fsid))
245245
print("DELETING OUTPUT SUBJECT DIR AND RE-RUNNING COMMAND:")
246246
print(cmd)
247247
run(cmd)
248-
elif os.path.isfile(os.path.join(output_dir, fsid, "mri/aseg.mgz")):
248+
elif os.path.isfile(os.path.join(output_dir, fsid, "label/BA_exvivo.thresh.ctab")):
249249
print("TEMPLATE ALREADY CREATED, SKIPPING")
250250
elif os.path.exists(os.path.join(output_dir, fsid)):
251251
print("SUBJECT DIR ALREADY EXISTS (without IsRunning.lh+rh), RUNNING COMMAND:")
@@ -254,8 +254,8 @@ def run(command, env={}, ignore_errors=False):
254254
else:
255255
print(cmd)
256256
run(cmd)
257-
258-
if ('longitudinal' in args.steps):
257+
258+
if 'longitudinal' in args.steps:
259259
for tp in timepoints:
260260
# longitudinally process all timepoints
261261
fsid = "sub-%s"%subject_label
@@ -271,7 +271,7 @@ def run(command, env={}, ignore_errors=False):
271271
print("DELETING OUTPUT SUBJECT DIR AND RE-RUNNING COMMAND:")
272272
print(cmd)
273273
run(cmd)
274-
elif os.path.isfile(os.path.join(output_dir, tp + ".long." + fsid, "mri/aseg.mgz")):
274+
elif os.path.isfile(os.path.join(output_dir, tp + ".long." + fsid, "label/BA_exvivo.thresh.ctab")):
275275
print("SUBJECT ALREADY SEGMENTED, SKIPPING")
276276
else:
277277
print(cmd)
@@ -328,6 +328,8 @@ def run(command, env={}, ignore_errors=False):
328328
print("DELETING OUTPUT SUBJECT DIR AND RE-RUNNING COMMAND:")
329329
print(cmd)
330330
run(cmd)
331+
elif os.path.isfile(os.path.join(output_dir, fsid, "label/BA_exvivo.thresh.ctab")):
332+
print("SUBJECT ALREADY SEGMENTED, SKIPPING")
331333
elif os.path.exists(os.path.join(output_dir, fsid)):
332334
print("SUBJECT DIR ALREADY EXISTS (without IsRunning.lh+rh), RUNNING COMMAND:")
333335
print(resume_cmd)
@@ -384,6 +386,8 @@ def run(command, env={}, ignore_errors=False):
384386
print("DELETING OUTPUT SUBJECT DIR AND RE-RUNNING COMMAND:")
385387
print(cmd)
386388
run(cmd)
389+
elif os.path.isfile(os.path.join(output_dir, fsid, "label/BA_exvivo.thresh.ctab")):
390+
print("SUBJECT ALREADY SEGMENTED, SKIPPING")
387391
elif os.path.exists(os.path.join(output_dir, fsid)):
388392
print("SUBJECT DIR ALREADY EXISTS (without IsRunning.lh+rh), RUNNING COMMAND:")
389393
print(resume_cmd)

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