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chrisgorgochrisgorgo
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Merge pull request #41 from BIDS-Apps/fix/parallel
Remove -parallel
2 parents 0ff9f93 + 0a8bcbb commit b63b6ce

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2 files changed

+10
-10
lines changed

2 files changed

+10
-10
lines changed

‎circle.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@ dependencies:
1616
- if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
1717
- if [[ ! -d ~/data/ds114_test1 ]]; then wget -c -O ${HOME}/ds114_test1.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e54a326c613b01d7d3ed90" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1.tar -C ${HOME}/data; fi
1818
- if [[ ! -d ~/data/ds114_test2 ]]; then wget -c -O ${HOME}/ds114_test2.tar "https://files.osf.io/v1/resources/9q7dv/providers/osfstorage/57e549f9b83f6901d457d162" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2.tar -C ${HOME}/data; fi
19-
- if [[ ! -d ~/data/ds114_test1_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar "https://osf.io/j6zk2/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi
20-
- if [[ ! -d ~/data/ds114_test2_freesurfer_precomp_v6.0.0 ]]; then wget -c -O ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar "https://osf.io/yhzzj/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi
19+
- if [[ ! -d ~/data/ds114_test1_freesurfer_precomp_v6.0.0 ]]; then wget -c --no-check-certificate -O ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar "https://osf.io/j6zk2/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test1_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi
20+
- if [[ ! -d ~/data/ds114_test2_freesurfer_precomp_v6.0.0 ]]; then wget -c --no-check-certificate -O ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar "https://osf.io/yhzzj/?action=download&version=1" && mkdir -p ${HOME}/data && tar xf ${HOME}/ds114_test2_freesurfer_precomp_v6.0.0.tar -C ${HOME}/data; fi
2121
- git describe --tags > version
2222
- docker build -t bids/${CIRCLE_PROJECT_REPONAME} . :
2323
timeout: 21600

‎run.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -224,12 +224,12 @@ def run(command, env={}, ignore_errors=False):
224224

225225
fsid = "sub-%s_ses-%s" % (subject_label, session_label)
226226
stages = " ".join(["-" + stage for stage in args.stages])
227-
cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid,
227+
cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
228228
output_dir,
229229
input_args,
230230
stages,
231231
args.n_cpus)
232-
resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid,
232+
resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid,
233233
output_dir,
234234
stages,
235235
args.n_cpus)
@@ -254,7 +254,7 @@ def run(command, env={}, ignore_errors=False):
254254
input_args = " ".join(["-tp %s" % tp for tp in timepoints])
255255
fsid = "sub-%s" % subject_label
256256
stages = " ".join(["-" + stage for stage in args.stages])
257-
cmd = "recon-all -base %s -sd %s %s %s -parallel -openmp %d" % (fsid,
257+
cmd = "recon-all -base %s -sd %s %s %s -openmp %d" % (fsid,
258258
output_dir,
259259
input_args,
260260
stages,
@@ -280,7 +280,7 @@ def run(command, env={}, ignore_errors=False):
280280
# longitudinally process all timepoints
281281
fsid = "sub-%s" % subject_label
282282
stages = " ".join(["-" + stage for stage in args.stages])
283-
cmd = "recon-all -long %s %s -sd %s %s -parallel -openmp %d" % (tp,
283+
cmd = "recon-all -long %s %s -sd %s %s -openmp %d" % (tp,
284284
fsid,
285285
output_dir,
286286
stages,
@@ -333,12 +333,12 @@ def run(command, env={}, ignore_errors=False):
333333

334334
fsid = "sub-%s" % subject_label
335335
stages = " ".join(["-" + stage for stage in args.stages])
336-
cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid,
336+
cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
337337
output_dir,
338338
input_args,
339339
stages,
340340
args.n_cpus)
341-
resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid,
341+
resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid,
342342
output_dir,
343343
stages,
344344
args.n_cpus)
@@ -391,12 +391,12 @@ def run(command, env={}, ignore_errors=False):
391391

392392
fsid = "sub-%s" % subject_label
393393
stages = " ".join(["-" + stage for stage in args.stages])
394-
cmd = "recon-all -subjid %s -sd %s %s %s -parallel -openmp %d" % (fsid,
394+
cmd = "recon-all -subjid %s -sd %s %s %s -openmp %d" % (fsid,
395395
output_dir,
396396
input_args,
397397
stages,
398398
args.n_cpus)
399-
resume_cmd = "recon-all -subjid %s -sd %s %s -parallel -openmp %d" % (fsid,
399+
resume_cmd = "recon-all -subjid %s -sd %s %s -openmp %d" % (fsid,
400400
output_dir,
401401
stages,
402402
args.n_cpus)

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