I am running into a problem with a Siemens dicom headers. I have collected scans with 2mm slice thickness and 2 mm gap between slices for 31 slices of the brain (31 dicom files) on a Siemens Trio system. When using the command spm_dicom_header to get header info I see the following parameters:
PixelSpacing=[3.7500;3.7500]
SliceThickness =2
SpacingBetweenSlices=2
1) This makes sense to me assuming they mean that SpacingBetweenSlices is the gap. If this field is really gap+thickness, then it is incorrect. What is meant by SpacingBetweenSlices (gap or gap+thickness)?
"Value of the prescribed spacing to be applied between the slices in a volume that is to be acquired. The spacing in mm is defined as the center-to-center distance of adjacent slices."
Additionally, when I use spm_dicom_convert the file to NIFTI and spm_vol to read the header, the matrix is the following:
-3.74643087387085 0 -0.0872387886047363 122.050718307495
0 3.75000000000000 0 -109.501228332520
-0.163572669029236 0 1.99809646606445 -45.6215378046036
0 0 0 1
2) Why is [1,1] = -3.74643087387085? I am guessing this value is calculated instead of pulling out 3.7500 from the header. Additionally, why is there a negative sign in front? Does this signify radiological acquisition vs neurological?
3) Why is the z value 1.99809646606445? I am assuming it is either taking into account only SliceThickness or that SpacingBetweenSlices really means gap+thickness, which is stored incorrectly. Any help would be appreciated.
M = [-3.74643087387085 0 -0.0872387886047363 122.0507183074950 3.75000000000000 0 -109.501228332520-0.163572669029236 0 1.99809646606445 -45.62153780460360 0 0 1];vox = sqrt(sum(M(1:3,1:3).^2))
vox =3.7500 3.7500 2.0000
I have also tried using other programs such as dcm2niigui and also still have the same issue with the z value showing 2mm instead of 4mm so I do not know if this is a general issue of storing slice gap correctly in nifti format or not reading it correctly from a Siemens dicom file. I know that there is NO NIFTI field for spacing between slices (assuming this means gap) in the Nifti-1.1 standards, but I wanted to see if others have ran into this issue and if so how you corrected it. One way around the issue is to correct the value from 1.998 to 4 and resave the matrix (resulting in qform warning), but I'd rather find the root cause and proper calculation in case this pops up again.