Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
F
fsl-pipe-example
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package Registry
Container Registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Michiel Cottaar
fsl-pipe-example
Compare revisions
e772ad21bb5dafeec388c3bd9bb55d9c45c71c18 to 0813ad8983ddb907d9c79d72e1ffb021bc87c18d
Compare revisions
Changes are shown as if the
source
revision was being merged into the
target
revision.
Learn more about comparing revisions.
Source
ndcn0236/fsl-pipe-example
Select target project
No results found
0813ad8983ddb907d9c79d72e1ffb021bc87c18d
Select Git revision
Branches
main
Swap
Target
ndcn0236/fsl-pipe-example
Select target project
ndcn0236/fsl-pipe-example
1 result
e772ad21bb5dafeec388c3bd9bb55d9c45c71c18
Select Git revision
Branches
main
Show changes
Only incoming changes from source
Include changes to target since source was created
Compare
Commits on Source (2)
Add config file for topup
· 95bdd4fc
Michiel Cottaar
authored
1 year ago
95bdd4fc
generate fake input data
· 0813ad89
Michiel Cottaar
authored
1 year ago
0813ad89
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
gen_input_data.sh
+14
-0
14 additions, 0 deletions
gen_input_data.sh
pipe.py
+1
-1
1 addition, 1 deletion
pipe.py
with
15 additions
and
1 deletion
gen_input_data.sh
0 → 100755
View file @
0813ad89
#!/usr/bin/env sh
mkdir
input
for
subject
in
100307 103818
;
do
directory
=
input/
${
subject
}
/unprocessed/3T/Diffusion
mkdir
-p
${
directory
}
for
dir
in
95 96 97
;
do
for
pe
in
LR RL
;
do
touch
${
directory
}
/
${
subject
}
_3T_DWI_dir
${
dir
}
_
${
pe
}
.nii.gz
touch
${
directory
}
/
${
subject
}
_3T_DWI_dir
${
dir
}
_
${
pe
}
.bval
touch
${
directory
}
/
${
subject
}
_3T_DWI_dir
${
dir
}
_
${
pe
}
.bvec
done
done
done
This diff is collapsed.
Click to expand it.
pipe.py
View file @
0813ad89
...
@@ -118,7 +118,7 @@ def run_topup(
...
@@ -118,7 +118,7 @@ def run_topup(
outfile
:
Out
(
"
fieldmap/fieldcoef
"
),
outfile
:
Out
(
"
fieldmap/fieldcoef
"
),
unwarped_b0
:
Out
,
unwarped_b0
:
Out
,
):
):
topup
(
merged_b0s
,
acqparams
,
out
=
topup_basename
,
iout
=
unwarped_b0
)
topup
(
merged_b0s
,
acqparams
,
out
=
topup_basename
,
iout
=
unwarped_b0
,
config
=
"
b02b0_1.cnf
"
)
# Let's have some simple recipes again
# Let's have some simple recipes again
...
...
This diff is collapsed.
Click to expand it.