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Fidel Alfaro Almagro
UK_biobank_pipeline_v_1.5
Commits
c11b063d
Commit
c11b063d
authored
Sep 20, 2021
by
Fidel Alfaro Almagro
Browse files
Update bb_pipeline_diff_queue_joint.py
parent
202ec8be
Changes
1
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Inline
Side-by-side
bb_diffusion_pipeline/bb_pipeline_diff_queue_joint.py
View file @
c11b063d
...
@@ -66,30 +66,30 @@ def bb_pipeline_diff_joint(subject, jobHold, fileConfiguration, queue, coeff,
...
@@ -66,30 +66,30 @@ def bb_pipeline_diff_joint(subject, jobHold, fileConfiguration, queue, coeff,
finalJob
=
"1"
finalJob
=
"1"
if
run_block_2
:
if
run_block_2
:
jobPREPARE
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_pre_eddy_'
+
subject
+
'" -j '
+
str
(
jobHold
)
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_pre_eddy '
+
subject
)
jobPREPARE
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_pre_eddy_'
+
subject
+
'" -j '
+
str
(
jobHold
)
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_pre_eddy '
+
subject
)
if
eddy_cpu
:
if
eddy_cpu
:
jobEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_eddy_cpu_'
+
subject
+
'" -j '
+
jobPREPARE
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_eddy_wrap_cpu '
+
baseDir
)
jobEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_eddy_cpu_'
+
subject
+
'" -j '
+
jobPREPARE
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_eddy_wrap_cpu '
+
baseDir
)
else
:
else
:
jobEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_eddy_gpu_'
+
subject
+
'" -j '
+
jobPREPARE
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_eddy_wrap_gpu '
+
baseDir
)
jobEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_eddy_gpu_'
+
subject
+
'" -j '
+
jobPREPARE
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_eddy_wrap_gpu '
+
baseDir
)
finalJob
=
finalJob
+
","
+
str
(
jobEDDY
)
finalJob
=
finalJob
+
","
+
str
(
jobEDDY
)
if
run_block_3
:
if
run_block_3
:
jobPOSTEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_post_eddy_'
+
subject
+
'" -j '
+
jobEDDY
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_post_eddy '
+
baseDir
+
' '
+
coeff
+
' '
+
str
(
b_value_shell
))
jobPOSTEDDY
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_post_eddy_'
+
subject
+
'" -j '
+
jobEDDY
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_eddy/bb_post_eddy '
+
baseDir
+
' '
+
coeff
+
' '
+
str
(
b_value_shell
))
jobDTIFIT
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_dtifit_'
+
subject
+
'" -j '
+
jobPOSTEDDY
+
' -l '
+
logDir
+
' ${FSLDIR}/bin/dtifit -k '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell -m '
+
baseDir
+
'/dMRI/dMRI/nodif_brain_mask_ud -r '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell.bvec -b '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell.bval -o '
+
baseDir
+
'/dMRI/dMRI/dti'
)
jobDTIFIT
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_dtifit_'
+
subject
+
'" -j '
+
jobPOSTEDDY
+
' -l '
+
logDir
+
' ${FSLDIR}/bin/dtifit -k '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell -m '
+
baseDir
+
'/dMRI/dMRI/nodif_brain_mask_ud -r '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell.bvec -b '
+
baseDir
+
'/dMRI/dMRI/data_ud_1_shell.bval -o '
+
baseDir
+
'/dMRI/dMRI/dti'
)
jobTBSS
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_tbss_'
+
subject
+
'" -j '
+
jobDTIFIT
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_tbss/bb_tbss_general '
+
subject
)
jobTBSS
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_tbss_'
+
subject
+
'" -j '
+
jobDTIFIT
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_tbss/bb_tbss_general '
+
subject
)
if
num_shells
>
1
:
if
num_shells
>
1
:
jobNODDI
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_NODDI_'
+
subject
+
'" -j '
+
jobTBSS
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_NODDI '
+
subject
)
jobNODDI
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_NODDI_'
+
subject
+
'" -j '
+
jobTBSS
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_NODDI '
+
subject
)
jobPREBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_pre_bedpostx_'
+
subject
+
'" -j '
+
jobDTIFIT
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_pre_bedpostx '
+
baseDir
+
'/dMRI/dMRI'
)
jobPREBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
short_queues
+
' -N "bb_pre_bedpostx_'
+
subject
+
'" -j '
+
jobDTIFIT
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_pre_bedpostx '
+
baseDir
+
'/dMRI/dMRI'
)
finalJob
=
finalJob
+
","
+
str
(
jobPREBEDPOSTX
)
finalJob
=
finalJob
+
","
+
str
(
jobPREBEDPOSTX
)
if
run_block_4
:
if
run_block_4
:
if
bedpostx_cpu
:
if
bedpostx_cpu
:
jobBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_bedpostx_cpu_'
+
subject
+
'" -j '
+
jobPREBEDPOSTX
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_bedpostx_cpu '
+
baseDir
+
'/dMRI/dMRI'
)
jobBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_bedpostx_cpu_'
+
subject
+
'" -j '
+
jobPREBEDPOSTX
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_bedpostx_cpu '
+
baseDir
+
'/dMRI/dMRI'
)
jobAUTOPTX
=
LT
.
runCommand
(
logger
,
'${BB_BIN_DIR}/bb_diffusion_pipeline/bb_autoPtx/bb_autoPtx_queue_cpu_joint '
+
subject
+
' '
+
jobBEDPOSTX
+
','
+
jobTBSS
+
' '
+
long_queues
)
jobAUTOPTX
=
LT
.
runCommand
(
logger
,
'${BB_BIN_DIR}/bb_diffusion_pipeline/bb_autoPtx/bb_autoPtx_queue_cpu_joint '
+
subject
+
' '
+
jobBEDPOSTX
+
','
+
jobTBSS
+
' '
+
long_queues
)
else
:
else
:
jobBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_bedpostx_gpu_'
+
subject
+
'" -j '
+
jobPREBEDPOSTX
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_bedpostx_gpu '
+
baseDir
+
'/dMRI/dMRI'
)
jobBEDPOSTX
=
LT
.
runCommand
(
logger
,
'${FSLDIR}/bin/fsl_sub -q '
+
long_queues
+
' -N "bb_bedpostx_gpu_'
+
subject
+
'" -j '
+
jobPREBEDPOSTX
+
' -l '
+
logDir
+
' $BB_BIN_DIR/bb_diffusion_pipeline/bb_bedpostx/bb_bedpostx_gpu '
+
baseDir
+
'/dMRI/dMRI'
)
jobAUTOPTX
=
LT
.
runCommand
(
logger
,
'${BB_BIN_DIR}/bb_diffusion_pipeline/bb_autoPtx/bb_autoPtx_queue_gpu_joint '
+
subject
+
' '
+
jobBEDPOSTX
+
','
+
jobTBSS
+
' '
+
long_queues
)
jobAUTOPTX
=
LT
.
runCommand
(
logger
,
'${BB_BIN_DIR}/bb_diffusion_pipeline/bb_autoPtx/bb_autoPtx_queue_gpu_joint '
+
subject
+
' '
+
jobBEDPOSTX
+
','
+
jobTBSS
+
' '
+
long_queues
)
finalJob
=
finalJob
+
","
+
str
(
jobAUTOPTX
)
finalJob
=
finalJob
+
","
+
str
(
jobAUTOPTX
)
...
...
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