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Christoph Arthofer
ms_templates
Commits
d19760f9
Commit
d19760f9
authored
Apr 21, 2021
by
Christoph Arthofer
Browse files
file permissions
parent
2921252d
Changes
2
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README.md
View file @
d19760f9
...
...
@@ -125,7 +125,45 @@ python run_template_construction.py
--gpuq
gpu8.q
```
## Output
Output directories will be automatically created for different purposes. These include:
#### `log`
Contains log-files from the job submission system; this is very useful for debugging
### `scripts`
Contains generated Bash and Python scripts e.g. for job array submissions, wrappers for Python functions
#### `affine_it1`
Contains the output of the first set of rigd and affine registrations including
-
rigid registrations between within-subject modalities (i.e. DTI to T2, T2 to T1)
-
affine registrations between each subject and a reference subject
-
unbiasing transformation removing the bias introduced by the reference subject
-
unbiased average T1 template in the unbiased space of the subjects
-
rigid transformation of unbiased template to MNI space
#### `affine_it1`
affine_it2 (affine_it2_dir)
{sub_id} (affine_it2_subject_dir)
T1_to_MNI152{ext_mat} (T1_to_MNI_mat)
T1_brain_to_MNI152{ext_nii} (T1_brain_to_MNI_img)
T1_head_to_MNI152{ext_nii} (T1_head_to_MNI_img)
T1_brain_mask_to_MNI152{ext_nii} (T1_brain_mask_to_MNI_img)
T2_FLAIR_to_MNI152{ext_mat} (T2_to_MNI_mat)
T2_FLAIR_brain_to_MNI152{ext_nii} (T2_brain_to_MNI_img)
T2_FLAIR_head_to_MNI152{ext_nii} (T2_head_to_MNI_img)
DTI_to_MNI152{ext_mat} (DTI_to_MNI_mat)
DTI_to_MNI152{ext_nii} (DTI_to_MNI_img)
DTI_tensor_to_MNI152{ext_nii} (DTI_tensor_to_MNI)
affine_template_T1_brain{ext_nii} (T1_brain_affine_template)
affine_template_T1_brain_mask{ext_nii} (T1_brain_mask_affine_template)
affine_template_T1_brain_mask_weighted{ext_nii} (T1_brain_mask_weighted_affine_template)
affine_template_T1_head{ext_nii} (T1_head_affine_template)
affine_template_T2_head{ext_nii} (T2_head_affine_template)
affine_template_DTI{ext_nii} (DTI_affine_template)
affine_template_DTI_tensor{ext_nii} (DTI_tensor_affine_template)
run_template_construction.py
View file @
d19760f9
...
...
@@ -278,7 +278,7 @@ def writeConfig(step,mod,fpath):
'fwhm_mov_tensor = 8.0 8.0 4.0 2.0 1.0 0.5 0.25
\n
'
\
'lambda_tensor = 1 1 1 1 1 1 1
\n
'
f
=
open
(
fpath
,
'w'
)
f
=
open
(
fpath
,
'w
+
'
)
f
.
write
(
s
)
f
.
close
()
...
...
@@ -501,7 +501,7 @@ def RMSdifference(img1_path, img2_path, mask1_path=None, mask2_path=None, rms_pa
print
(
'RMS difference between {} and {}: {}'
.
format
(
img1_path
,
img2_path
,
rms
))
if
rms_path
is
not
None
:
with
open
(
rms_path
,
'w'
)
as
f
:
with
open
(
rms_path
,
'w
+
'
)
as
f
:
f
.
write
(
'{}'
.
format
(
rms
))
...
...
@@ -544,7 +544,7 @@ def RMSstandardDeviation(img_paths, mean_img_path, mask_path, sd_img_out_path=No
print
(
'RMS standard deviation: {}'
.
format
(
rms
))
if
rms_out_path
is
not
None
:
with
open
(
rms_out_path
,
'w'
)
as
f
:
with
open
(
rms_out_path
,
'w
+
'
)
as
f
:
f
.
write
(
'{}'
.
format
(
rms
))
...
...
@@ -739,18 +739,18 @@ if __name__ == "__main__":
job_ids
=
[
''
for
_
in
range
(
100
)]
task_count
=
0
os
.
mkdir
(
base_dir
,
mode
=
0o7
0
0
)
if
not
os
.
path
.
exists
(
base_dir
)
else
print
(
base_dir
+
' exists'
)
os
.
chmod
(
base_dir
,
0o7
0
0
)
os
.
mkdir
(
base_dir
,
mode
=
0o7
7
0
)
if
not
os
.
path
.
exists
(
base_dir
)
else
print
(
base_dir
+
' exists'
)
os
.
chmod
(
base_dir
,
0o7
7
0
)
tree
=
FileTree
.
read
(
tree_path
,
top_level
=
''
)
tree
=
tree
.
update
(
data_dir
=
data_dir
,
template_dir
=
base_dir
)
script_dir
=
tree
.
get
(
'script_dir'
)
os
.
mkdir
(
script_dir
,
mode
=
0o7
0
0
)
if
not
os
.
path
.
exists
(
script_dir
)
else
print
(
script_dir
+
' exists'
)
os
.
mkdir
(
script_dir
,
mode
=
0o7
7
0
)
if
not
os
.
path
.
exists
(
script_dir
)
else
print
(
script_dir
+
' exists'
)
log_dir
=
tree
.
get
(
'log_dir'
)
os
.
mkdir
(
log_dir
,
mode
=
0o7
0
0
)
if
not
os
.
path
.
exists
(
log_dir
)
else
print
(
log_dir
+
' exists'
)
os
.
mkdir
(
log_dir
,
mode
=
0o7
7
0
)
if
not
os
.
path
.
exists
(
log_dir
)
else
print
(
log_dir
+
' exists'
)
misc_dir
=
tree
.
get
(
'misc_dir'
)
os
.
mkdir
(
misc_dir
,
mode
=
0o7
0
0
)
if
not
os
.
path
.
exists
(
misc_dir
)
else
print
(
misc_dir
+
' exists'
)
os
.
mkdir
(
misc_dir
,
mode
=
0o7
7
0
)
if
not
os
.
path
.
exists
(
misc_dir
)
else
print
(
misc_dir
+
' exists'
)
shutil
.
copyfile
(
identity_path
,
tree
.
get
(
'identity_mat'
))
ref_idx
=
0
...
...
@@ -783,7 +783,7 @@ if __name__ == "__main__":
# Soft clamping of high skull intensities
task_name
=
'{:03d}_prep_clamping'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
)
T1_head_path
=
tree
.
get
(
mod
[
'T1_head_key'
])
...
...
@@ -803,7 +803,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_registrations_2_ref'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
...
...
@@ -822,7 +822,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_registrations_T2_2_T1'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
id
)
cmd
=
flirt
(
tree
.
get
(
mod
[
'T2_brain_key'
]),
tree
.
get
(
mod
[
'T1_brain_key'
]),
omat
=
tree
.
get
(
'T2_to_T1_mat'
),
...
...
@@ -837,7 +837,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_registrations_DTI_2_T2'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
id
)
cmd
=
flirt
(
tree
.
get
(
mod
[
'DTI_scalar_key'
]),
tree
.
get
(
mod
[
'T2_brain_key'
]),
omat
=
tree
.
get
(
'DTI_to_T2_mat'
),
...
...
@@ -873,7 +873,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_unbiased_transform_of_T1'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
mod
[
'T1_brain_key'
]),
ref
=
affine_ref_path
,
mat
=
tree
.
get
(
'T1_to_unbiased_mat'
),
...
...
@@ -889,7 +889,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_concat_T2_and_unbiased'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
concatxfm
(
tree
.
get
(
'T2_to_T1_mat'
),
tree
.
get
(
'T1_to_unbiased_mat'
),
...
...
@@ -905,7 +905,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_concat_DTI_and_unbiased'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
concatxfm
(
tree
.
get
(
'DTI_to_T2_mat'
),
tree
.
get
(
'T2_to_unbiased_mat'
),
...
...
@@ -943,7 +943,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_concat_T1_brain_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
concatxfm
(
tree
.
get
(
'T1_to_unbiased_mat'
),
tree
.
get
(
'T1_unbiased_affine_template_to_MNI_mat'
),
...
...
@@ -959,7 +959,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_concat_T2_brain_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
concatxfm
(
tree
.
get
(
'T2_to_unbiased_mat'
),
tree
.
get
(
'T1_unbiased_affine_template_to_MNI_mat'
),
...
...
@@ -975,7 +975,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_concat_DTI_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
concatxfm
(
tree
.
get
(
'DTI_to_unbiased_mat'
),
tree
.
get
(
'T1_unbiased_affine_template_to_MNI_mat'
),
...
...
@@ -991,7 +991,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_transform_T1_brain_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
mod
[
'T1_brain_key'
]),
ref
=
mni_path
,
mat
=
tree
.
get
(
'T1_to_MNI_mat'
),
...
...
@@ -1007,7 +1007,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_transform_T1_brain_masks_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
mod
[
'T1_brain_mask_key'
]),
ref
=
mni_path
,
...
...
@@ -1024,7 +1024,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_transform_T1_head_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
'T1_head_clamped'
),
ref
=
mni_path
,
mat
=
tree
.
get
(
'T1_to_MNI_mat'
),
...
...
@@ -1040,7 +1040,7 @@ if __name__ == "__main__":
task_name
=
'{:03d}_affT_transform_T2_head_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
if
mod
[
'T2_head_key'
]
is
not
None
:
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
mod
[
'T2_head_key'
]),
ref
=
mni_path
,
mat
=
tree
.
get
(
'T2_to_MNI_mat'
),
...
...
@@ -1056,7 +1056,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_transform_DTI_scalar_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
applyxfm
(
src
=
tree
.
get
(
mod
[
'DTI_scalar_key'
]),
ref
=
mni_path
,
mat
=
tree
.
get
(
'DTI_to_MNI_mat'
),
...
...
@@ -1072,7 +1072,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_affT_transform_DTI_tensor_to_MNI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
ref_id
=
aff_ref_id
)
cmd
=
'vecreg -i '
+
tree
.
get
(
mod
[
'DTI_tensor_key'
])
+
\
...
...
@@ -1233,7 +1233,7 @@ if __name__ == "__main__":
# Nonlinear registration to template from previous iteration
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
export_vars
=
{}
for
i
,
id
in
enumerate
(
ls_ids
):
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
...
...
@@ -1344,7 +1344,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_resample_warps'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
warp_path
=
tree
.
get
(
'mmorf_warp'
)
...
...
@@ -1361,7 +1361,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_unbias_warps'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
f
.
write
(
'fslmaths '
+
tree
.
get
(
'mmorf_warp_resampled'
)
+
' -add '
+
tree
.
get
(
...
...
@@ -1375,7 +1375,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_concat_unbiased_warps_T1_brain'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
full_resampled_path
=
tree
.
get
(
'mmorf_warp_resampled_unbiased_full_T1brain'
)
...
...
@@ -1394,7 +1394,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_concat_unbiased_warps_T1_head'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
full_resampled_path
=
tree
.
get
(
'mmorf_warp_resampled_unbiased_full_T1head'
)
...
...
@@ -1413,7 +1413,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_concat_unbiased_warps_T2_head'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
full_resampled_path
=
tree
.
get
(
'mmorf_warp_resampled_unbiased_full_T2'
)
...
...
@@ -1432,7 +1432,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_concat_unbiased_warps_DTI'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
full_resampled_path
=
tree
.
get
(
'mmorf_warp_resampled_unbiased_full_DTI'
)
...
...
@@ -1452,7 +1452,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_warp_T1_brain'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
img_path
=
tree
.
get
(
mod
[
'T1_brain_key'
])
...
...
@@ -1470,7 +1470,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_warp_T1_brain_mask'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
img_path
=
tree
.
get
(
mod
[
'T1_brain_mask_key'
])
...
...
@@ -1493,7 +1493,7 @@ if __name__ == "__main__":
T1_head_key_temp
=
mod
[
'T1_head_key'
]
else
:
T1_head_key_temp
=
'T1_head_clamped'
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
img_path
=
tree
.
get
(
T1_head_key_temp
)
...
...
@@ -1512,7 +1512,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_warp_T2_head'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
img_path
=
tree
.
get
(
mod
[
'T2_head_key'
])
...
...
@@ -1531,7 +1531,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_warp_DTI_scalar'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
img_path
=
tree
.
get
(
mod
[
'DTI_scalar_key'
])
...
...
@@ -1550,7 +1550,7 @@ if __name__ == "__main__":
task_count
+=
1
task_name
=
'{:03d}_nlnT_warp_DTI_tensor'
.
format
(
task_count
)
script_path
=
os
.
path
.
join
(
script_dir
,
task_name
+
'.sh'
)
with
open
(
script_path
,
'w'
)
as
f
:
with
open
(
script_path
,
'w
+
'
)
as
f
:
for
id
in
ls_ids
:
tree
=
tree
.
update
(
sub_id
=
id
,
step_id
=
'{:02d}'
.
format
(
step
),
it_id
=
'{:02d}'
.
format
(
it
))
cmd
=
'vecreg -i '
+
tree
.
get
(
'data/DTI_tensor'
)
+
\
...
...
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