save matrix into .nii or .img file

Hello,

I have .nii file which I filtered basing on distance criteria; now I have a list of filtered coordinates

like this : file =

MNI_x MNI_y MNI_z Z_value

50 -4 -46 4.1706

50 -2 -46 4.1706

50 0 -46 4.1706

54 -6 -44 4.1706

52 -6 -44 4.1706

50 -6 -44 4.1706

54 -4 -44 4.1706

52 -4 -44 4.1706

can anyone please help me to find a way to save those filtered coordinates in to .img or .nii file.

[Priyanka Gorijala]

I tried this

output=make_nii(file);

>> save_nii(output,'myfile.nii');

>> nii= load_nii('myfile.nii');

>> view_nii(nii);

but it doesn't work; showing empty image

[Rik]

Have you read the documentation for those functions? Did they contain any examples? Were you able to reproduce those?

[Priyanka Gorijala]

I read, but I am not able to reproduce those.

So I am trying for something which converts matrix to .img or .nii file

Answer 1

[Omar Salah]

Marsbar toolbox have ready made functions for that. http://marsbar.sourceforge.net/ you would usually construct a roi first with the coordinates using the object constructor called "maroi_pointlist" then save them with another function.

Here is what I use in my code:

img_mat = maroi_pointlist(struct('XYZ',<COORDINATES>,'vals',<VALUES>,'roithresh',0,'binarize',0,'mat',<Inversion matrix (I got it from SPM)>,'descrip','', 'label', <Label> ),'vox');       
img_roi=saveroi(img_mat,  <IMAGENAME>);
save_as_image(img_roi, <IMAGENAME>);