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What input params need to be changed to get this running?
def basc_run(subjects_list, basc_config):
import os
import numpy as np
import nibabel as nib
import yaml
from basc.basc_workflow_runner import run_basc_workflow
from pathlib import Path
subject_file_list= subjects_list
try:
FSLDIR = os.environ['FSLDIR']
except NameError:
print('FSLDIR environment variable not set!')
##Determine the voxel size from sample subject's func image affine to pull correct MNI_152 image
bna_img = nib.load(subject_file_list[0])
x_vox = np.diagonal(bna_img.affine[:3,0:3])[0]
y_vox = np.diagonal(bna_img.affine[:3,0:3])[1]
z_vox = np.diagonal(bna_img.affine[:3,0:3])[2]
if x_vox <= 1 and y_vox <= 1 and z_vox <=1:
roi_mask_file = FSLDIR + '/data/standard/MNI152_T1_1mm_brain.nii.gz'
else:
roi_mask_file = FSLDIR + '/data/standard/MNI152_T1_2mm_brain.nii.gz'
basc_config=Path(__file__).parent/'basc_config.yaml'
f = open(basc_config)
basc_dict_yaml=yaml.load(f)
basc_dict =basc_dict_yaml['instance']
proc_mem=basc_dict['proc_mem']
dataset_bootstraps= basc_dict['dataset_bootstraps']
timeseries_bootstraps= basc_dict['timeseries_bootstraps']
n_clusters= basc_dict['n_clusters']
output_size= basc_dict['output_size']
bootstrap_list= eval(basc_dict['bootstrap_list'])
cross_cluster= basc_dict['cross_cluster']
affinity_threshold= basc_dict['affinity_threshold']
out_dir= Path(__file__).parent/'rsnrefs'
run= basc_dict['run']
similarity_metric= basc_dict['similarity_metric']
run_basc_workflow(subject_file_list, roi_mask_file, dataset_bootstraps, timeseries_bootstraps, n_clusters, output_size, bootstrap_list, proc_mem, similarity_metric, cross_cluster=cross_cluster, roi2_mask_file=None, affinity_threshold=affinity_threshold, out_dir=out_dir, run=run)
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