[Neuroimaging] Getting scaling and offset from nifti header in nibabel
Samuel St-Jean
stjeansam at gmail.com
Mon Jan 4 09:43:03 EST 2016
That is a good question which I am also trying to find an answer to.
Actually, what are the slope and inter field specifically referring to?
I know that for some reason the scanner likes to recast everything between
0 and 4096 (probably for storage reason), so you cannot mix and match
acquisitions from the same session but acquired in different block because
of that.
Because of some scaling (which I think might be slope and inter), it also
means that your magnitude/phase data has weird values (which make no sense
for the phase data), but correcting for this scaling from the dicom headers
fix it.
This field (which has a private tag for philips, but I can try to dig it
out from somewhere with pydicom) let's you indeed recover sane values, so I
was wondering if it is related to the slope and inter field from the nifti
file, thus no need to dig it out from the dicom. The whole point if this
nifti field is the same as the one in the dicom, I could dump my custom,
half-baked dicom converter for problematic files and just scale the
converted nifti myself (provided a converter works, magnitude/phase data
are so seldom used that I have no tool working on those, if anyone has
suggestions.)
Didn't know about the dataobj thing though, thanks for pointing it out.
2015-12-17 18:57 GMT+01:00 Matthew Brett <matthew.brett at gmail.com>:
> Hi,
>
> On Thu, Dec 17, 2015 at 4:42 PM, Samuel St-Jean <stjeansam at gmail.com>
> wrote:
> > 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.
>
> No - nothing wrong. The nibabel reader resets the scale and slope to
> NaN by default when it reads in the image.
>
> If you want to read the original scale and slope, you can get them
> from the image array proxy object, as in:
>
> img.dataobj.slope
> img.dataobj.inter
>
> Is that what you needed?
>
> Matthew
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> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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