Cleaning up

adbartni · Mar 30, 2021 · 9af04c7 · 9af04c7
1 parent b7ccdd5
commit 9af04c7
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Showing 20 changed files with 19 additions and 15 deletions.
diff --git a/.gitignore b/.gitignore
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/__init__.py b/__init__.py
diff --git a/activate b/activate
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-source /shared/studies/nonregulated/connectome/fmri/preprocessing_pipeline/venv/bin/activate
+source /shared/nonrestricted/connectome/fmri/preprocessing_pipeline/venv/bin/activate
diff --git a/collect_raw_data/__init__.py b/collect_raw_data/__init__.py
diff --git a/collect_raw_data/collect_raw_data.py b/collect_raw_data/collect_raw_data.py
@@ -15,7 +15,7 @@ def init_fmri_subject_dir(subjectID, path_fmri, path_HCP):
 
     ## Copy QSM data to fmri subject directory
     strippedID = subjectID[2:]
-    path_QSM = os.path.join("/shared/studies/nonregulated/qsm_repo/data/", strippedID + "/recon/")
+    path_QSM = os.path.join("/shared/nonrestricted/qsm_repo/data/", strippedID + "/recon/")
     if os.path.isdir(path_QSM) and not os.path.exists(path_fmri + subjectID + "/phase_combined.nii.gz"):
         for qsm_file in ["magnitude_combined.nii.gz", "phase_combined.nii.gz"]:
             copyfile(os.path.join(path_QSM, qsm_file), os.path.join(path_fmri, subjectID + "/" + qsm_file))

diff --git a/connectome_analyses/FunctionalConnectivity.py b/connectome_analyses/FunctionalConnectivity.py
@@ -14,8 +14,8 @@ class FunctionalConnectome:
 
     def __init__(self, subjectID):
         self.subjectID = subjectID
-        self.path_fmri = "/shared/studies/nonregulated/connectome/fmri/subjects/" + subjectID + "/"
-        self.path_HCP = "/shared/studies/nonregulated/connectome/Subjects/" + subjectID + "/T1w/"
+        self.path_fmri = "/shared/nonrestricted/connectome/fmri/subjects/" + subjectID + "/"
+        self.path_HCP = "/shared/nonrestricted/connectome/Subjects/" + subjectID + "/T1w/"
 
     def create_functional_connectivity_matrix(self):
         """ Performs functional connectivity analysis on a subject

diff --git a/connectome_analyses/__init__.py b/connectome_analyses/__init__.py
diff --git a/main.py b/main.py
@@ -58,8 +58,8 @@ def pipeline(self):
             try:
                 if self.phase == "premelodic":
                     init_fmri_subject_dir(subjectID,
-                                          "/shared/studies/nonregulated/connectome/fmri/subjects/",
-                                          "/shared/studies/nonregulated/connectome/Subjects/" + subjectID + "/T1w/")
+                                          "/shared/nonrestricted/connectome/fmri/subjects/",
+                                          "/shared/nonrestricted/connectome/Subjects/" + subjectID + "/T1w/")
 
                     processing = Preprocessing(subjectID)
                     structproc = StructuralProcessing(processing)
@@ -112,8 +112,8 @@ def pipeline(self):
                     <<< DON'T USE THIS UNTIL FIX IS WORKING >>> 
                     """
                     init_fmri_subject_dir(subjectID,
-                                           "/shared/studies/nonregulated/connectome/fmri/subjects/",
-                                           "/shared/studies/nonregulated/connectome/Subjects/" + subjectID + "/T1w/")
+                                           "/shared/nonrestricted/connectome/fmri/subjects/",
+                                           "/shared/nonrestricted/connectome/Subjects/" + subjectID + "/T1w/")
 
                     processing = Preprocessing(subjectID)
                     structproc = StructuralProcessing(processing)
@@ -173,10 +173,10 @@ def starting_files_present(subjectID):
         before beginning processing
     """
 
-    path_conntectome = "/shared/studies/nonregulated/connectome/"
+    path_conntectome = "/shared/nonrestricted/connectome/"
     functional_data = path_conntectome + "fmri/subjects/" + subjectID + "/rawfunc.nii.gz"
     structural_data = path_conntectome + "Subjects/" + subjectID + "/T1w/T1w_acpc_dc_restore_brain.nii.gz"
-    QSM_path = "/shared/studies/nonregulated/qsm_repo/data/" + subjectID.replace("EX","") + "/recon/"
+    QSM_path = "/shared/nonrestricted/qsm_repo/data/" + subjectID.replace("EX","") + "/recon/"
 
     if (not os.path.exists(functional_data)
             or not os.path.exists(structural_data)

diff --git a/match_function_by_name.py b/match_function_by_name.py
@@ -42,3 +42,4 @@ def match(subjectID, function):
 if __name__ == "__main__":
         function = match("EX54589", "epi_distortion_correction")
         print(function)
+
diff --git a/preprocessing/Melodic.py b/preprocessing/Melodic.py
@@ -32,7 +32,7 @@ def init_melodic_directory(self):
                 copyfile(self.path_fmri + cp_file,
                         self.path_fmri + "denoise.ica/" + cp_file)
         if not os.path.exists(self.path_fmri + "denoise.ica/design.fsf"):
-            copyfile("/shared/studies/nonregulated/connectome/fmri/subjects/design.fsf",
+            copyfile("/shared/nonrestricted/connectome/fmri/subjects/design.fsf",
                     self.path_fmri + "denoise.ica/design.fsf")
 
         for cp_dir in dirs:

diff --git a/preprocessing/PostMelodicProcessing.py b/preprocessing/PostMelodicProcessing.py
diff --git a/preprocessing/PreMelodicProcessing.py b/preprocessing/PreMelodicProcessing.py
@@ -21,8 +21,8 @@ class Preprocessing:
 
     def __init__(self, subjectID):
         self.subjectID = subjectID
-        self.path_fmri = "/shared/studies/nonregulated/connectome/fmri/subjects/" + subjectID + "/"
-        self.path_HCP = "/shared/studies/nonregulated/connectome/Subjects/" + subjectID + "/T1w/"
+        self.path_fmri = "/shared/nonrestricted/connectome/fmri/subjects/" + subjectID + "/"
+        self.path_HCP = "/shared/nonrestricted/connectome/Subjects/" + subjectID + "/T1w/"
         self.mc_path = "/shared/software/vendor/freesurfer/freesurfer-5.3.0_x86_64/bin/"
         self.ants_path = "/usr/lib/ants/"
 

diff --git a/preprocessing/StructuralProcessing.py b/preprocessing/StructuralProcessing.py
diff --git a/preprocessing/__init__.py b/preprocessing/__init__.py
diff --git a/quality_control/init_reports_directory.py b/quality_control/init_reports_directory.py
@@ -8,7 +8,7 @@
 with open(subject_list_file) as infile:
     subject_list = infile.read().splitlines()
 
-path_fmri = '/shared/studies/nonregulated/connectome/fmri/subjects/'
+path_fmri = '/shared/nonrestricted/connectome/fmri/subjects/'
 
 if not os.path.isdir('reports'):
     os.mkdir('reports')

diff --git a/quality_control/registration_report.py b/quality_control/registration_report.py
@@ -4,11 +4,13 @@
 import os
 
 
+# Creates a string of all the filenames of T1 and registered functional images
+# to feed into ImageMagick
 subjects_as_string = ""
 for subjectID in subject_list:
 
     reg_func_file = path_fmri + subjectID + "/ants/epi2braints.nii.gz"
-    t1_file = "/shared/studies/nonregulated/connectome/Subjects/" + subjectID + \
+    t1_file = "/shared/nonrestricted/connectome/Subjects/" + subjectID + \
             "/T1w/T1w_acpc_dc_restore_brain_2.00.nii.gz"
     if os.path.exists(reg_func_file) and os.path.exists(t1_file):
 
@@ -33,5 +35,6 @@
 
     #break
 
+# Creates a pdf of functional images overlaid on T1 for all subjects
 os.system("convert " + subjects_as_string + " reports/missing_subs_epi2struct.pdf")
 
diff --git a/requirements.in b/requirements.in
Original file line number	Diff line number	Diff line change
Expand Up		@@ -42,3 +42,4 @@ def match(subjectID, function):
		if __name__ == "__main__":
		function = match("EX54589", "epi_distortion_correction")
		print(function)