Merge pull request #204 from pni-lab/94-wrong-input_dir-in-example-sc…

…ripts Fix wrong input_dir specifications
pni-lab · Jan 17, 2025 · ea7cdbf · ea7cdbf
2 parents 8ad36f3 + 5904a9b
commit ea7cdbf
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Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/examples/bet_bids_func_subworkflow.py b/examples/bet_bids_func_subworkflow.py
@@ -35,7 +35,7 @@ def bet_wf(wf, **kwargs):
 
 if __name__ == '__main__':
     ROOT_DIR = os.path.dirname(os.getcwd())
-    input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+    input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
     output_dir = os.path.join(ROOT_DIR,
                               'data_out')  # path where the folder 'BET' will be created for the results of this script
     working_dir = os.path.join(ROOT_DIR,

diff --git a/examples/bet_bids_subworkflow.py b/examples/bet_bids_subworkflow.py
@@ -6,7 +6,7 @@
 
 if __name__ == '__main__':
     ROOT_DIR = os.path.dirname(os.getcwd())
-    input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+    input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
     output_dir = os.path.join(ROOT_DIR,
                               'data_out')  # path where the folder 'BET' will be created for the results of this script
     working_dir = os.path.join(ROOT_DIR,

diff --git a/examples/defacing_ex_bids.py b/examples/defacing_ex_bids.py
@@ -6,7 +6,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR,
                           'data_out')  # path where the folder 'BET' will be created for the results of this script
 working_dir = os.path.join(ROOT_DIR,

diff --git a/examples/despiking_bids_ex.py b/examples/despiking_bids_ex.py
@@ -4,7 +4,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR,
                           'data_out')  # path where the folder 'BET' will be created for the results of this script
 working_dir = os.path.join(ROOT_DIR,

diff --git a/examples/ex_bids_pipeline.py b/examples/ex_bids_pipeline.py
@@ -3,7 +3,7 @@
 from nipype import Function
 
 # experiment specific parameters:
-input_dir = 'data_in/bids'  # place where the bids data is located
+input_dir = 'data_in/pumi-unittest'  # place where the bids data is located
 output_dir = 'data_out'  # place where the folder 'BET' will be created for the results of this script
 working_dir = 'data_out'  # place where the folder 'bet_iter_wf' will be created for the workflow
 

diff --git a/examples/ex_compcor.py b/examples/ex_compcor.py
@@ -8,7 +8,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the folder with the results of this script
 working_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the workflow folder
 

diff --git a/examples/ex_func_proc.py b/examples/ex_func_proc.py
@@ -10,7 +10,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the folder with the results of this script
 working_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the workflow folder
 

diff --git a/examples/ex_func_to_anat_bids.py b/examples/ex_func_to_anat_bids.py
@@ -7,7 +7,7 @@
 
 # experiment specific parameters:
 ROOT_DIR = os.path.dirname(os.getcwd())
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # place where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # place where the bids data is located
 output_dir = os.path.join(ROOT_DIR, 'data_out')  # place where the folder will be created for the results of this script
 working_dir = os.path.join(ROOT_DIR, 'data_out')  # place where the folder will be created for the workflow
 

diff --git a/examples/ex_tmpfilt.py b/examples/ex_tmpfilt.py
@@ -10,7 +10,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the folder with the results of this script
 working_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the workflow folder
 

diff --git a/examples/rpn_preproc.py b/examples/rpn_preproc.py
@@ -11,7 +11,7 @@
 
 ROOT_DIR = os.path.dirname(os.getcwd())
 
-input_dir = os.path.join(ROOT_DIR, 'data_in/bids')  # path where the bids data is located
+input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest')  # path where the bids data is located
 output_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the folder with the results of this script
 working_dir = os.path.join(ROOT_DIR, 'data_out')  # path for the workflow folder