Hi,
I am running into the same problem where a 2d+t image I saved as nii is being recognized as having one dimension by AFNI. In AFNI gui, I see other data as 'epan:3D+t:528' (2d slice over a single slice for 528 time points) but this nii shows up as 'abuc:1' which prevents it from being used as an input for 3ddeconvolve I am trying to do.
I've ran nifti_tool as instructed:
N-1 header file 'CO2_ASL_2d_whole.nii', num_fields = 43
all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr 0 1 348
data_type 4 10
db_name 14 18
extents 32 1 0
session_error 36 1 0
regular 38 1
dim_info 39 1 0
dim 40 8 3 64 64 262 1 1 1 1
intent_p1 56 1 0.0
intent_p2 60 1 0.0
intent_p3 64 1 0.0
intent_code 68 1 0
datatype 70 1 64
bitpix 72 1 64
slice_start 74 1 0
pixdim 76 8 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
vox_offset 108 1 352.0
scl_slope 112 1 1.0
scl_inter 116 1 0.0
slice_end 120 1 0
slice_code 122 1 0
xyzt_units 123 1 0
cal_max 124 1 0.0
cal_min 128 1 0.0
slice_duration 132 1 0.0
toffset 136 1 0.0
glmax 140 1 0
glmin 144 1 0
descrip 148 80
aux_file 228 24
qform_code 252 1 0
sform_code 254 1 2
quatern_b 256 1 0.0
quatern_c 260 1 0.0
quatern_d 264 1 0.0
qoffset_x 268 1 0.0
qoffset_y 272 1 0.0
qoffset_z 276 1 0.0
srow_x 280 4 1.0 0.0 0.0 0.0
srow_y 296 4 0.0 1.0 0.0 0.0
srow_z 312 4 0.0 0.0 1.0 0.0
intent_name 328 16
magic 344 4 n+1
The dim entries seem right because I want 3d datat of 64x64 matrix over 262 time points. I 've used the following to generate this nii file in python:
new_image = nibabel.Nifti1Image(ASL_2d_whole, affine=np.eye(4))
nibabel.save(new_image, 'E'+En_CO2+'_afni/CO2_ASL_2d_whole.nii')
Could you help me understand what might have gone wrong with this way of generating nifti format image?
