[NEW] Initialize project.

.gitignore

@@ -0,0 +1,27 @@
+# Python Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Python distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Mac OS-specific storage files
+.DS_Store

README.md

@@ -0,0 +1,41 @@
+# Pantheon
+
+Pantheon is a series of functions and workflows aimed to facilitate analyzing fMRI data. It
+provides a unified api to access and manipulate data in a custom layout. It also includes workflows
+to create HCP-like data (e.g., functional dtseries data in fsLR 32k space) from fMRIPrep outputs.
+
+This project is created to meet my own data analysis requirement and preference. It may not
+reflect the best practices. But it will constantly evolve with my latest thoughts.
+
+## Getting Started
+
+This project mostly relies on python packages. But several common neuroimaging tools are also
+required to complete certain operations.
+
+### Dependencies
+
+Python
+- Required
+    - numpy
+    - pandas
+    - nibabel
+    - nilearn
+    - rpy2
+- Optional
+    - rpy2
+    - plotly
+
+Neuroimaging tools
+- AFNI
+- FSL
+- FreeSurfer
+- Workbench
+
+
+## License
+
+Distributed under the MIT License.
+
+## Contact
+
+Zhifang Ye - [email protected]

pantheon/__init__.py

@@ -0,0 +1,2 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-

pantheon/data/atlas_example.yaml

@@ -0,0 +1,20 @@
+---
+fsLR:
+  MMP1:
+    L: data/external/atlas/MMP1/S1200_space-fsLR_den-32k_desc-MMP1_dseg.dlabel.nii
+    R: data/external/atlas/MMP1/S1200_space-fsLR_den-32k_desc-MMP1_dseg.dlabel.nii
+  MMP1_Subcortical:
+    L: data/external/atlas/MMP1/S1200_space-MNI152NLin2009cAsym_res-02_desc-MMP1_dseg.nii.gz
+    R: data/external/atlas/MMP1/S1200_space-MNI152NLin2009cAsym_res-02_desc-MMP1_dseg.nii.gz
+fsaverage:
+  Brainnetome:
+    L: data/external/atlas/Brainnetome/fsaverage.L.BN_Atlas.32k_fs_LR.label.gii
+    R: data/external/atlas/Brainnetome/fsaverage.R.BN_Atlas.32k_fs_LR.label.gii
+MNI152NLin6Asym:
+  Template_ASeg:
+    L: data/external/atlas/Template_ASeg/MNI_space-MNI152NLin6Asym_res-2_desc-Subcortical_dseg.nii.gz
+    R: data/external/atlas/Template_ASeg/MNI_space-MNI152NLin6Asym_res-2_desc-Subcortical_dseg.nii.gz
+T1w:
+  Custom:
+    L: data/external/atlas/Custom/{sub_id}/{sub_id}_hemi-L.label.gii
+    R: data/external/atlas/Custom/{sub_id}/{sub_id}_hemi-R.label.gii

pantheon/data/data_validation_example.yaml

@@ -0,0 +1,13 @@
+task:
+  task-encoding:
+    run_list: [run-1, run-2] # a list indicates all possible runs
+    exclude:
+      sub-023: [run-1] # map subject and runs need to be excluded
+  task-retrieval:
+    run_list: [run-1, run-2, run-3]
+    exclude: {}
+  task-movie:
+    run_list: [] # an empty list for task with only one scan
+    exclude:
+      sub-005: [] # leave the run list empty
+exclude_subject: [sub-001]