the colin27 samples do not specify the offset (translation) in the SForm

[robertoostenveld]

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

[fangq]

The issue was caused by the fact that these .jnii/.bnii files were generated from a generic 3D array from a .mat file using this script
https://github.com/fangq/jnifti/blob/master/samples/colin27/create_jnii.m

so the header was created from scratch using jniicreate().

I added this line to manually fix this issue: https://github.com/fangq/jnifti/blob/master/samples/colin27/create_jnii.m#L4

however, a better solution would be coping the .nii.gz file and load from it to keep all the original nii headers.