I have used python to analyse some fMRI data and would now like to save my results as niftis that I can then use in an SPM analysis.
My data scores is an array of float64 of shape (97, 115, 97). I have used the following code to save it:
import nibabel as nib
import nilearn
scores_image = nib.Nifti1Image(scores,affine = np.eye(4))
nib.save(scores_image,"scores.nii")
However, when I load the data into SPM I notice that both the origin and the scale are different from what SPM is expecting: Comparison of my scores.nii (upper image) and a standard SPM nifti
Does anyone know which code would automatically save my scores variable with the same origin and size as SPM is expecting?
Update: Here is the header of an SPM image with highlight where it differs from my own image:
comp_img = nib.load('spmT_0014.nii')
print(comp_img.header)
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr : 348
data_type : b''
db_name : b''
extents : 0
session_error : 0
regular : b'r' ## ---> b''
dim_info : 0
dim : [ 3 97 115 97 1 1 1 1]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : float32
bitpix : 32
slice_start : 0
pixdim : [1. 2. 2. 2. 0. 0. 0. 0.] ## ---> [1. 1. 1. 1. 1. 1. 1. 1.]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 10 ## ---> 0
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0
glmax : 0
glmin : 0
descrip : b''
aux_file : b''
qform_code : aligned ## ---> unknown
sform_code : aligned
quatern_b : 0.0
quatern_c : 0.0
quatern_d : 0.0
qoffset_x : -96.5 ## ---> 0
qoffset_y : -132.5 ## ---> 0
qoffset_z : -78.5 ## ---> 0
srow_x : [ 2. 0. 0. -96.5] ## ---> [1. 0. 0. 0.]
srow_y : [ 0. 2. 0. -132.5] ## ---> [0. 1. 0. 0.]
srow_z : [ 0. 0. 2. -78.5] ## ---> [0. 0. 1. 0.]
intent_name : b''
magic : b'n+1'
I have found a way to do this by using the following code:
from nilearn import image
import nibabel as nib
comp_img = nib.load('spmT_0014.nii')
scores_img = image.new_img_like(comp_img, scores, copy_header=False)
Which gives me the following (upper image is the SPM one and lower image is the one I created):