AnatomicalProcessing.md

Processing anatomical images

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Freesurfer Anatomical Processing

Run Freesurfer with freesurfer_to_vols.sh

To run this on biowulf, go to the base directory for the subject & run with an sbatch command (replace sub-?? with the subject ID)

Qwarp non-linear alignment

Run QwarpAlign.sh ${subj} to run AFNI's auto_warp.py.
This script's function is a wrapper to submit the command to the biowulf cluster.

QwarpAlign.sh sub-??

Outputs:
Qwarped anatomicals located in the subject's Proc_Anat directory

Pre-process fMRI data with run_afniproc.sh

This afni_proc.py runs QA analyses of each subject after scanning

run_afniproc.sh sub-??

Output:
afni_proc.py directories/files for WNW/Breathing/Movie runs

Generate statistical maps from GLM variations with Make_GLM_swarm.sh

Make_GLM_swarm.sh sub-??

Output:
The following GLMs located in the GLMs directory: OC_mot_CSF, OC_mot, e2_mot_CSF, septedana_mot, septedana_mot_csf, orthtedana_mot_csf, orthtedana_mot, combined_regressors

see the main ../README.md for more details on what these GLMs are

Generate the functionally localized ROIs with Func2ROI.sh

Func2ROI.sh sub-??

Output:
sub-??.FuncROIs.nii.gz (and other useful files)