I am creating my own NIfTI data sets from ascii values based on the header definition in the nifti1.h header file. When I check the values actually written with hexdump against the text file, they are correct in both position and value. When I view them with the Afni gui, however, the values are different from what I see elsewhere. They do not even follow a scaling factor that I can tell. The position for non-zero values is correct, however, so I know that I'm not just looking in the wrong place.
My question is, why is AFNI modifying the values when it displays them in its GUI, and how can I get it to stop doing this? Here is the NIfTI header for a sample file:
nifti_type = 'NIFTI-1+'
header_filename = 'estimates__harvard_vs_iowa__estimate.nii'
image_filename = 'estimates__harvard_vs_iowa__estimate.nii'
image_offset = '348'
ndim = '3'
nx = '41'
ny = '48'
nz = '35'
dx = '4'
dy = '4'
dz = '4'
datatype = '16'
datatype_name = 'FLOAT32'
nvox = '68880'
nbyper = '4'
byteorder = 'MSB_FIRST'
intent_code = '3'
intent_code_name = 'T-statistic'
intent_p1 = '7.84727e-44'
intent_p2 = '0'
intent_p3 = '0'
xyz_units = '2'
xyz_units_name = 'mm'
descrip = 'FSL3.2beta'
qform_code = '3'
qform_code_name = 'Talairach'
qto_xyz_matrix = '-4 0 -0 80 0 4 -0 -112 0 0 4 -52 0 0 0 1'
qto_ijk_matrix = '-0.25 0 -0 20 0 0.25 0 28 -0 -0 0.25 13 0 0 0 1'
quatern_b = '0'
quatern_c = '1'
quatern_d = '0'
qoffset_x = '80'
qoffset_y = '-112'
qoffset_z = '-52'
qfac = '-1'
qform_i_orientation = 'Right-to-Left'
qform_j_orientation = 'Posterior-to-Anterior'
qform_k_orientation = 'Inferior-to-Superior'
sform_code = '3'
sform_code_name = 'Talairach'
sto_xyz_matrix = '-4 0 0 80 0 4 0 -112 0 0 4 -52 0 0 0 1'
sto_ijk matrix = '-0.25 0 -0 20 0 0.25 -0 28 -0 -0 0.25 13 0 0 0 1'
sform_i_orientation = 'Right-to-Left'
sform_j_orientation = 'Posterior-to-Anterior'
sform_k_orientation = 'Inferior-to-Superior'
