[Neuroimaging] Getting scaling and offset from nifti header in nibabel

[Samuel St-Jean]

 Hello,

I'd like to get the scaling and offset value to compare data from two
volumes acquired in the same scan. Since the floating points values are
wildly different, we need ot put them on the same scaling of intensity.
This can be done from the dicom files directly, but it a painful and error
prone process and difficult to automate.

Turns out mrconvert from mrtrix does not take into account scaling when
your data is in floating point (by design, so even the options to correct
this scaling are disabled), but still stores the correct values. When
opening the nifti files converted from nibabel the headers just show nan
values, while mrtrix can parse them correctly. Here is the header from
mrinfo as an example.

************************************************
Image:               "noise.nii.gz"
************************************************
  Format:            NIfTI-1.1
  Dimensions:        128 x 128 x 78
  Voxel size:        1.79665 x 1.79665 x 1.8
  Dimension labels:  0. left->right (mm)
                     1. posterior->anterior (mm)
                     2. inferior->superior (mm)
  Data type:         signed 16 bit integer (little endian)
  Data layout:       [ -0 -1 +2 ]
  Data scaling:      offset = 0, multiplier = 166.825
  Comments:          SAMUEL 9JUIL (SAMU
                     MRtrix version: 0.3.12-1050-g62ace960
  Transform:               0.9993    -0.00287    -0.03691 -115.6
                       -5.649e-11       0.997    -0.07752 -108.4
                          0.03702     0.07746      0.9963 -60.36
                                0           0           0 1

Same header through nibabel

<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr      : 348
data_type       :
db_name         : SAMUEL 9JUIL (SAMU
extents         : 16384
session_error   : 0
regular         : r
dim_info        : 0
dim             : [  3 128 128  78   1   1   1   1]
intent_p1       : 0.0
intent_p2       : 0.0
intent_p3       : 0.0
intent_code     : none
datatype        : int16
bitpix          : 16
slice_start     : 0
pixdim          : [ 1.          1.79665172  1.79665172  1.79999924
0.          0.          0.
  0.        ]
vox_offset      : 0.0
scl_slope       : nan
scl_inter       : nan
slice_end       : 0
slice_code      : unknown
xyzt_units      : 10
cal_max         : 0.0
cal_min         : 0.0
slice_duration  : 0.0
toffset         : 0.0
glmax           : 0
glmin           : 0
descrip         : MRtrix version: 0.3.12-1050-g62ace960
aux_file        :
qform_code      : scanner
sform_code      : scanner
quatern_b       : -0.0185005571693
quatern_c       : -0.038780156523
quatern_d       : 0.999076247215
qoffset_x       : 111.719642639
qoffset_y       : 119.12978363
qoffset_z       : -34.2374076843
srow_x          : [ -1.79541993e+00   5.15606394e-03 -6.64402023e-02
1.11719643e+02]
srow_y          : [  1.01492648e-10  -1.79124594e+00 -1.39527366e-01
1.19129784e+02]
srow_z          : [ -0.06651677  -0.13917242   1.79335308 -34.23740768]
intent_name     :
magic           : n+1


Those would probably be scl_slope and scl_inter, but the values just got
lost somewhere apparently. The same behavior is seen from the example in
nifti header here :
http://nipy.org/nibabel/nifti_images.html#the-nifti-header

So the questions

1. Did something went wrong, or do both program just use different field?
If so, does nibabel show all fields in the header or only known ones?
2. Is the field scl_slope/scl_inter even related to the dicom scaling (and
offset/multiplier from mrtrix, though this one goes in their mailing list
if nobody knows)? Philips call those SS and SI values, and you simply need
to fix the offset + scaling with these numbers to get sane intensities out
of your scanner, but they are a huge pain to get out.

Thanks,

Samuel
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20151217/a53e971a/attachment.html>