SOP.md

Standard Operating Procedure

Preprocessing Workflow Structure

1. process_study

Creating WM and GM Histograms by Masking

1. create_masked_files
2. create_individual_histograms_of_images.py

RAVEL

See RAVEL.

1. The CSF mask file is here /home/feczk001/shared/projects/S1067_Loes/data/MNI152/mni_icbm152_nlin_sym_09a/

2. You have to create a CSF masked file for each input file. You can do that with this code.

3. Create a control region for RAVEL. Here is example code.

4. Run RAVEL on files. You can see an example of how to do this here.