code to run NMRI225 template construction as described in "Big Field of View MRI T1w and FLAIR Template - NMRI225" by Kreilkamp et al. 2023, Scientific Data.
Make a folder structure like this: HOME_DIRECTORY/storage/SUBJECT_ID/anat/SUBJECT_ID.hrT1.nii HOME_DIRECTORY/storage/SUBJECT_ID/anat/SUBJECT_ID.hrT1.json HOME_DIRECTORY/storage/SUBJECT_ID/anat/SUBJECT_ID.hrFLAIR.nii HOME_DIRECTORY/storage/SUBJECT_ID/anat/SUBJECT_ID.hrFLAIR.json
Run NMRI225_run.m If necessary, modify line 20 "cfg.group='controls';"
Run NMRI225_run.py Possibly modify lines 45-55 to reflect where your data, MNI template and MNI_BIG_FOV files are: root_dir=os.path.join(os.getenv("NMRI_PROJECTS"),"nfocke","controls_pool")
MNI_tmpl_file=os.path.join(os.getenv("NMRI_TOOLS"),"fsl",os.getenv("FSLVERSION"),"data","standard","MNI152_T1_1mm.nii.gz") MNI_tmpl_05_file=os.path.join(os.getenv("NMRI_TOOLS"),"fsl",os.getenv("FSLVERSION"),"data","standard","MNI152_T1_0.5mm.nii.gz")
MNI_BIG_FOV_file=os.path.join(root_dir,"templates","MNI_BIG_FOV.nii") MNI_BIG_FOV_05_file=os.path.join(root_dir,"templates","MNI_BIG_FOV_05.nii") MNI_BIG_FOV_brainmask_file=os.path.join(root_dir,"templates","MNI_BIG_FOV.brain.mask.nii") MNI_BIG_FOV_mask_file=os.path.join(root_dir,"templates","MNI_BIG_FOV.mask.nii")