create_ROI_using_MNI

python code:

http://www.jonaskaplan.com/lab/files/make_roi_sphere.py

#Creates a spherical ROI from a single coordinate
#
#Jonas Kaplan
#[e-mail]
#July 2014
#

from __future__ import division
import argparse
import os
from subprocess import call

#parse command line arguments
parser = argparse.ArgumentParser(description="create spherical ROIs from coordinate")
parser.add_argument("x",help="x coordinate")
parser.add_argument("y",help="y coordinate")
parser.add_argument("z",help="z coordinate")
parser.add_argument("radius",help="radius in mm")
parser.add_argument("filename",help="output file name")
parser.add_argument("--mm",help="coordinates are mm coordinates in MNI space instead of voxel coordinates",action="store_true")
args = parser.parse_args()

def mmToVox(mmcoords):
    #function to convert mm coordinates in the standard 2mm MNI atlas into voxel coordinates
    voxcoords = ['','','']
    voxcoords[0] = str(int(round(int(mmcoords[0])/2))*-1+45)
    voxcoords[1] = str(int(round(int(mmcoords[1])/2))+63)
    voxcoords[2] = str(int(round(int(mmcoords[2])/2))+36)
    return voxcoords


coords =[args.x,args.y,args.z]

if args.mm:
    #convert from mm to voxel coords
    voxcoords = mmToVox(coords)
else:
    voxcoords = coords

outfile = args.filename

command = "fslmaths $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask -roi %s 1 %s 1 %s 1 0 1 tmp" % (voxcoords[0],voxcoords[1],voxcoords[2])
print command
call(command,shell=True)

command = "fslmaths tmp -kernel sphere %s -fmean tmp" % (args.radius)
print command
call(command,shell=True)

command = "fslmaths tmp -thr .00001 -bin %s" % outfile
print command
call(command,shell=True)

command = "rm tmp.nii.gz"
call(command,shell=True)

matlab

need to convert to mm

you have selected point pt = [x0,y0,z0] and radius r

https://www.reddit.com/r/matlab/comments/1198rn/creating_a_spherical_region_of_interest_from_a/

% vol is your volume, rad is your radius, vox is the 1x3
% coordinates of the center voxel
[x y z] = ind2sub(size(vol),1:numel(vol));
M = [x y z] - repmat(vox,numel(vol),1);
D = reshape(sqrt(sum(M.^2,2)) <= rad,size(vol)); 
voxels = find(D);
% D is a boolean array, the same size as the volume, such that 
% every voxel in the ROI is '1' and 0 otherwise. 
% voxels is a list of indicies such that vol(voxels) returns the value 
% of the voxels that are included in the roi

or

[X,Y,Z]=meshgrid(X,Y,Z); % X, Y, Z the sampling along each dimension
dist=sqrt((X-x0).^2+(Y-y0).^2+(Z-z0).^2);
sphere_data = data(dist<r);