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the colin27_zlib.bnii sample has an uint8 Affine matrix
>> jnii = loadjnifti('colin27_zlib.bnii')
jnii =
struct with fields:
NIFTIHeader: [1×1 struct]
NIFTIData: [181×217×181 uint8]
>> jnii.NIFTIHeader.Affine
ans =
3×4 uint8 matrix
1 0 0 0
1 0 0 0
1 0 0 0
I guess that the the srow_x, srow_y and srow_z arrays are used to make the Affine matrix. According to https://brainder.org/2012/09/23/the-nifti-file-format/ these arrays should be float (i.e., single precision).
Looking more critically at the correspondence between nifti and jnifti, I would actually say that there should not be a 3x4 Affine array, but that it should have the 1x4 srow_x, srow_y and srow_z arrays.
the colin27 samples do not specify the offset (translation) in the SForm
this is what I expect
>> mri = ft_read_mri('~/matlab/fieldtrip/template/anatomy/single_subj_T1_1mm.nii')
the coordinate system appears to be 'scanras'
mri =
struct with fields:
dim: [181 217 181]
anatomy: [181×217×181 double]
hdr: [1×1 struct]
transform: [4×4 double]
unit: 'mm'
>> mri.transform
ans =
1 0 0 -91
0 1 0 -127
0 0 1 -73
0 0 0 1
and this is what I get
>> mri = ft_read_mri('colin27_zlib.jnii')
mri =
struct with fields:
hdr: [1×1 struct]
anatomy: [181×217×181 uint8]
dim: [181 217 181]
unit: 'mm'
coordsys: 'scanras'
transform: [4×4 double]
>> mri.transform
ans =
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
Package JNIfTI toolbox for Fedora
This is on-going.
NeuroFedora pagure tracker:
https://pagure.io/neuro-sig/NeuroFedora/issue/298
Package spec file:
https://github.com/fangq/fedorapkg/tree/jnifti
Redhat new package review request:
https://bugzilla.redhat.com/show_bug.cgi?id=1758007
GNU Octave Image package
Are there plans to integrate the niftiread, niftiwrite and niftiinfo routines in GNU Octave Image toolbox?
https://savannah.gnu.org/patch/?9853
the colin27_zlib.bnii sample file has an incorrect Affine matrix
>> jnii = loadjnifti('colin27_zlib.bnii')
jnii =
struct with fields:
NIFTIHeader: [1×1 struct]
NIFTIData: [181×217×181 uint8]
>> jnii.NIFTIHeader.Affine
ans =
3×4 uint8 matrix
1 0 0 0
1 0 0 0
1 0 0 0
I had expected it to be eye(3,4), consistent with the colin27_zlib.jnii sample.
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