Home

Github Project link

This project contains code to support 4 GUIs/freesurfer commands.

1. fiducials_calibration
2. fiducials_correction
3. retrospective_correction
4. connected_components

NOTE: For more information on how to use these GUIs, please refer to freesurfer wiki

Path on calico: /space/calico/1/users/Harsha/photo-calibration-gui

Python Environment:

• Option 1. Build your own using the requirements file.
• Option 2. Source my environment- source /space/calico_001/users/Harsha/venvs/gui-venv/bin/activate
• Option 3: Source freesurfer source /usr/local/freesurfer/nmr-dev-env-bash

NOTE: If you source freesurfer, use fspython instead of python wherever appropriate.

Project Structure:

Directory Structure:

• Makefile - Contains recipes to run various GUIs
• misc - This directory contains python scripts for the old GUIs (that can be safely ignored) and a segmentation script for binary masking.
• README.md
• requirements.txt - Project requirements
• resources - This directory contains the horizontal and vertical ruler
• scripts - This directory contains func_{fs_command}.py files that drive each of the aforementioned freesurfer commands.

If you want to run each of these functions, you can either:

1. Run them in debug mode (in an IDE), or
2. You can invoke the corresponding target in the Makefile. For example: run make fiducials_calibration from the commandline.