Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Christoph Arthofer
ms_templates
Commits
29c37353
Commit
29c37353
authored
Apr 14, 2021
by
Christoph Arthofer
Browse files
upgraded to new version of Filetree
parent
2de507c6
Changes
2
Hide whitespace changes
Inline
Side-by-side
config/MS_template.tree
View file @
29c37353
...
...
@@ -3,9 +3,9 @@ ext_mat=.mat
ext_ini=.ini
ext_txt=.txt
{data_dir}
!
{data_dir}
->data (data)
{template_dir}
!
{template_dir}
misc (misc_dir)
ident{ext_mat} (identity_mat)
log (log_dir)
...
...
@@ -69,6 +69,7 @@ ext_txt=.txt
nln_template_T1_brain_mask_{step_id}_{it_id}{ext_nii} (T1_brain_mask_nln_template)
nln_template_T1_brain_mask_weighted_{step_id}_{it_id}{ext_nii} (T1_brain_mask_weighted_nln_template)
nln_template_T1_brain_SD_{step_id}_{it_id}{ext_nii} (T1_brain_SD_nln_template)
nln_template_T1_head_SD_{step_id}_{it_id}{ext_nii} (T1_head_SD_nln_template)
nln_template_T1_head_{step_id}_{it_id}{ext_nii} (T1_head_nln_template)
nln_template_T2_head_{step_id}_{it_id}{ext_nii} (T2_head_nln_template)
nln_template_DTI_{step_id}_{it_id}{ext_nii} (DTI_nln_template)
...
...
run_template_construction.py
View file @
29c37353
...
...
@@ -15,8 +15,8 @@ import nibabel as nib
import
numpy
as
np
from
fsl.wrappers
import
fslmaths
,
flirt
,
applyxfm
,
concatxfm
,
bet
,
fast
,
fslstats
from
fsl.wrappers.fnirt
import
invwarp
,
applywarp
,
convertwarp
#
from file_tree import FileTree
from
fsl.utils.filetree
import
FileTree
from
file_tree
import
FileTree
#
from fsl.utils.filetree import FileTree
from
fsl.utils.fslsub
import
func_to_cmd
from
operator
import
itemgetter
import
tempfile
...
...
@@ -433,7 +433,6 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
@return The job ID.
"""
cmd
=
'fsl_sub'
if
wait_for
and
any
(
job
!=
''
for
job
in
wait_for
):
cmd
+=
' -j '
...
...
@@ -466,7 +465,6 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
return
job_id
def
RMSdifference
(
img1_path
,
img2_path
,
mask1_path
=
None
,
mask2_path
=
None
,
rms_path
=
None
):
"""! Calculates the difference between two images or warps as the root mean squared (RMS)
...
...
@@ -748,7 +746,7 @@ if __name__ == "__main__":
os
.
mkdir
(
base_dir
,
mode
=
0o700
)
if
not
os
.
path
.
exists
(
base_dir
)
else
print
(
base_dir
+
' exists'
)
os
.
chmod
(
base_dir
,
0o700
)
tree
=
FileTree
.
read
(
tree_path
,
directory
=
''
)
tree
=
FileTree
.
read
(
tree_path
,
top_level
=
''
)
tree
=
tree
.
update
(
data_dir
=
data_dir
,
template_dir
=
base_dir
)
script_dir
=
tree
.
get
(
'script_dir'
)
...
...
@@ -1215,7 +1213,7 @@ if __name__ == "__main__":
img_ref_T1brain_path
=
tree
.
get
(
'T1_brain_affine_template'
)
img_ref_T1head_path
=
tree
.
get
(
'T1_head_affine_template'
)
img_ref_T2head_path
=
tree
.
get
(
'T2_head_affine_template'
)
img_ref_tensor_path
=
tree
.
get
(
'
DTI_tensor
_affine_template'
)
img_ref_tensor_path
=
tree
.
get
(
'
T1_head
_affine_template'
)
img_ref_T1brain_mask_path
=
tree
.
get
(
'T1_brain_mask_weighted_affine_template'
)
else
:
if
it
==
1
:
...
...
@@ -1229,7 +1227,7 @@ if __name__ == "__main__":
img_ref_T1brain_path
=
tree
.
get
(
'T1_brain_nln_template'
)
img_ref_T1head_path
=
tree
.
get
(
'T1_head_nln_template'
)
img_ref_T2head_path
=
tree
.
get
(
'T2_head_nln_template'
)
img_ref_tensor_path
=
tree
.
get
(
'
DTI_tensor
_nln_template'
)
img_ref_tensor_path
=
tree
.
get
(
'
T1_head
_nln_template'
)
img_ref_T1brain_mask_path
=
tree
.
get
(
'T1_brain_mask_weighted_nln_template'
)
avgwarp_prev_it_path
=
tree
.
get
(
'avg_warp'
)
avgmask_prev_it_path
=
tree
.
get
(
'T1_brain_mask_nln_template'
)
...
...
@@ -1706,7 +1704,7 @@ if __name__ == "__main__":
tmp_dir
=
script_dir
,
kwargs
=
None
,
clean
=
"never"
)
job_ids
[
52
]
=
submitJob
(
tag
+
'_'
+
task_name
,
log_dir
,
command
=
jobcmd
,
queue
=
cpuq
,
wait_for
=
[
job_ids
[
44
]]
)
wait_for
=
list
(
itemgetter
(
*
[
44
,
49
])(
job_ids
))
)
print
(
'submitted: '
+
task_name
)
# RMS of intensity standard deviation of individual images in template space
...
...
@@ -1718,14 +1716,14 @@ if __name__ == "__main__":
img_paths
.
append
(
tree
.
get
(
'warped_T1brain'
))
jobcmd
=
func_to_cmd
(
RMSstandardDeviation
,
args
=
(
img_paths
,
tree
.
get
(
'T1_
brain
_nln_template'
),
tree
.
get
(
'T1_
head
_nln_template'
),
tree
.
get
(
'T1_brain_mask_nln_template'
),
tree
.
get
(
'T1_
brain
_SD_nln_template'
),
tree
.
get
(
'T1_
head
_SD_nln_template'
),
tree
.
get
(
'sd_intensity_output'
)),
tmp_dir
=
script_dir
,
kwargs
=
None
,
clean
=
"never"
)
job_ids
[
53
]
=
submitJob
(
tag
+
'_'
+
task_name
,
log_dir
,
command
=
jobcmd
,
queue
=
cpuq
,
wait_for
=
[
job_ids
[
44
]]
)
wait_for
=
list
(
itemgetter
(
*
[
45
,
49
])(
job_ids
))
)
print
(
'submitted: '
+
task_name
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment