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31_count_locations.py
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31_count_locations.py
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"""
count # of locations reported across all papers
- for response to PLOS reviews
"""
import numpy as N
from mniconvert import *
import nibabel as nib
import os
peakfiledir='/corral-repl/utexas/poldracklab/data/textmining/paper/data_preparation/peakfiles'
nfiles=5809
if 0:
data=N.zeros((60,72,60))
focictr=0
for f in range(nfiles):
d=N.loadtxt(os.path.join(peakfiledir,'peaks_%05d.txt'%int(f+1)),ndmin=2)
#####################
# read coordinates and add to dataset
for cnum in range(len(d)):
MNI_coords=d[cnum]
voxel_coords=convert_MNI_to_voxel_coords(MNI_coords,3)
if validate_voxel_coords(voxel_coords,3)==0:
#print 'coord not valid:', voxel_coords
continue
else:
data[voxel_coords[0]][voxel_coords[1]][voxel_coords[2]]=1
focictr+=1
mni_template='/work/01329/poldrack/software_lonestar/atlases/MNI152lin_3mm_mask_dil2mm.nii.gz'
template=nib.load(mni_template)
newimg=nib.Nifti1Image(data,template.get_affine())
newimg.to_filename('foci_data.nii.gz')