DOCUMENTATION FOR SWEGLE ET AL., TOWARDS MAPPING CSF VOLUME CHANGE AT HIGH RESOLUTIONS AT 7T, 2024

Scripts:

This folder contains the scripts used to process the imaging data.

Here is information on how to run these scripts:

1. Run conv_nih.sh on all files
2. The following step was done because file names were wrong:
   • Sort files into folders by run, examples: run1, run2, run3
   • Run rename_constrasts.sh on each run folder
3. Sort by TI and TE combinations, so make nine folders total, examples: TI1_TE1, TI2_TE3, TI3_TE1
   • Make sure each file contains its correct run number before moving the files out of the run folders
4. Run either SPM motion correction or AFNI motion correction
   • SPM motion correction:
     • Run SPM_moco_bold.sh on each of the nine folders
     • Run mocobatch_bold.m on each of the nine folders
   • Or, AFNI motion correction:
     • Run AFNI_moco_bold_nii.sh in each of the 9 folders
5. If doing NORDIC:
   • Run NORDIC_wrapper_edited.sh
6. Combine runs:
   • If NORDIC run: combine_NORDIC_runs_3TI_3TE_SPM.sh
   • If not NORDIC run: combine_runs_3TI_3TE_SPM.sh
7. To make time course maps:
   • Run make_timecourse_edited copy_final.sh

Scan Parameters:

This folder contains information about the scan parameters generally used for the scans in this project.