Adding support for sform and qform matrices as fields within the loaded nifti file header.

[divital-coder]

Is there a possibility to add support for sform and qform matrices as fields within the NIfTI.NIfTI1Header type?

[Tokazama]

Since the header is a reflection of the actually storage format it won't change to store a literal matrix (although sqform is pretty close already). We could make it easier to interact with it as if it were a matrix though. Similar to how Rotations.jl has array like rotation objects.

[divital-coder]

Okay so similar to a matrix but not the julia matrix itself, wondering if you were referring to the quaterns and srow values for interacting as if theyu were q and s form matrices... is that something that you were trying to entail

[Tokazama]

wondering if you were referring to the quaterns and srow values for interacting as if theyu were q and s form matrices...

Yeah, that's what I was referring to. At the same time, I'm not sure how that interface would really work in terms of the header struct itself. I think it makes more sense to extract those matrices from the header with a function than build them into it though. I'm not totally against it if you have a killer idea though.

[divital-coder]

So originally i asked this question, because i had to forumalte a nifti struct again after loading a nifti file using NIfTi.jl, following the nifti1io.h nifti image structure, cuz they include things like grid dimensions, spacings,
`
/*! \struct nifti_image
\brief High level data structure for open nifti datasets in the
nifti1_io API. Note that this structure is not part of the
nifti1 format definition; it is used to implement one API
for reading/writing formats in the nifti1 format.
/
typedef struct { /!< Image storage struct **/

int ndim ; /!< last dimension greater than 1 (1..7) /
int nx ; /!< dimensions of grid array /
int ny ; /!< dimensions of grid array /
int nz ; /!< dimensions of grid array /
int nt ; /!< dimensions of grid array /
int nu ; /!< dimensions of grid array /
int nv ; /!< dimensions of grid array /
int nw ; /!< dimensions of grid array /
int dim[8] ; /!< dim[0]=ndim, dim[1]=nx, etc. /
size_t nvox ; /!< number of voxels = nxnynz...nw /
int nbyper ; /!< bytes per voxel, matches datatype /
int datatype ; /!< type of data in voxels: DT_ code */

float dx ; /*!< grid spacings /
float dy ; /!< grid spacings /
float dz ; /!< grid spacings /
float dt ; /!< grid spacings /
float du ; /!< grid spacings /
float dv ; /!< grid spacings /
float dw ; /!< grid spacings /
float pixdim[8] ; /!< pixdim[1]=dx, etc. */

float scl_slope ; /*!< scaling parameter - slope /
float scl_inter ; /!< scaling parameter - intercept */

float cal_min ; /*!< calibration parameter, minimum /
float cal_max ; /!< calibration parameter, maximum */

int qform_code ; /*!< codes for (x,y,z) space meaning /
int sform_code ; /!< codes for (x,y,z) space meaning */

int freq_dim ; /*!< indexes (1,2,3, or 0) for MRI /
int phase_dim ; /!< directions in dim[]/pixdim[] /
int slice_dim ; /!< directions in dim[]/pixdim[] */

int slice_code ; /*!< code for slice timing pattern /
int slice_start ; /!< index for start of slices /
int slice_end ; /!< index for end of slices /
float slice_duration ; /!< time between individual slices */

/*! quaternion transform parameters
[when writing a dataset, these are used for qform, NOT qto_xyz] */
float quatern_b , quatern_c , quatern_d ,
qoffset_x , qoffset_y , qoffset_z ,
qfac ;

mat44 qto_xyz ; /*!< qform: transform (i,j,k) to (x,y,z) /
mat44 qto_ijk ; /!< qform: transform (x,y,z) to (i,j,k) */

mat44 sto_xyz ; /*!< sform: transform (i,j,k) to (x,y,z) /
mat44 sto_ijk ; /!< sform: transform (x,y,z) to (i,j,k) */

float toffset ; /*!< time coordinate offset */

int xyz_units ; /!< dx,dy,dz units: NIFTI_UNITS_ code /
int time_units ; /!< dt units: NIFTI_UNITS_* code */

int nifti_type ; /*!< 0==ANALYZE, 1==NIFTI-1 (1 file),
2==NIFTI-1 (2 files),
3==NIFTI-ASCII (1 file) /
int intent_code ; /!< statistic type (or something) /
float intent_p1 ; /!< intent parameters /
float intent_p2 ; /!< intent parameters /
float intent_p3 ; /!< intent parameters /
char intent_name[16] ; /!< optional description of intent data */

char descrip[80] ; /*!< optional text to describe dataset /
char aux_file[24] ; /!< auxiliary filename */

char fname ; /!< header filename (.hdr or .nii) */
char iname ; /!< image filename (.img or .nii) /
int iname_offset ; /!< offset into iname where data starts /
int swapsize ; /!< swap unit in image data (might be 0) /
int byteorder ; /!< byte order on disk (MSB_ or LSB_FIRST) /
void data ; /!< pointer to data: nbypernvox bytes */

int num_ext ; /*!< number of extensions in ext_list /
nifti1_extension * ext_list ; /!< array of extension structs (with data) /
analyze_75_orient_code analyze75_orient; /!< for old analyze files, orient */

} nifti_image ;`

like the above

[divital-coder]

so if thats some that can be added, do let me know i will figure out how to do that within this package :)
would love to contribute

[divital-coder]

also if thats something not ideal, i can figure out other ways to make them interact as a matrix

[Tokazama]

I have code laying around somewhere that can help with that. I have a lot of work I have to do at the present time so it's all dependent on if I can get away doing this sort of stuff during meetings where I'm simply supposed to be looking attentive.

[divital-coder]

ok great, but have you taken a look at the grid spacing and dimensions of grid array
those are the ones i wanted to emphasize upon, also i totally understand your indulgences for the time being, i am very much interested in Nifti.jl cuz i have been using it for the past month or so :)
thanks for building such functional and operational package, u are awesome