Thanks!

I forgot to set the qform_code, so avwhd was basically ignoring all the
other fields because qform_code was 0.

One more question - what does fslview do with this orientation
information. How are the images displayed, and what is the definition
of the axes in fslview? (what is +x, +y and +z and where is it on the
screen)?

thanks

zrinka
On Mar 26, 2005, at 2:59 AM, Mark Jenkinson wrote:

> Hi Zrinka,
>
> What we do in avwhd is show what is effectively read into our i/o
> library from the nifti file.  It doesn't show all the fields in the
> same
> format as the nifti1.h file, partly so they are more human readable.
> So, for instance, we shown qform_code and qform_name where
> the latter is the ascii string associated with the former.  So only
> qform_code is stored in the file, and the qform_name is completely
> determined from the qform_code.  Similarly for qto_xyz which
> show the affine matrix associated with the quaternion parameters,
> since the quaternions themselves are much less human friendly.
>
> So it looks like you are doing the right thing, except that if you
> want to have valid qforms in the file, then you should set the
> qform_code to something other than 0 (which represents 'Unknown').
>
> Also, note that our i/o was based on code written by Bob Cox, and
> modified by me.  You are welcome to reuse this code yourself or
> make your own modifications.  There will also be a 'reference library'
> based on this code coming from the nifti data format working group
> soon, which also might help.
>
> Hope this clears things up for you.
> All the best,
>    Mark
>
>
>
>
> Zrinka Bilusic wrote:
>
>> Hello!
>> I am working on some code that creates nifti images (the nifti pair)
>> and I was trying to use avwhd
>> to read the header infromation to test my code. My code is based on
>> the information in the nifti
>> spec file (http://nifti.nimh.nih.gov/pub/dist/src/nifti1.h) and some
>> sample code from Bob Cox.
>>
>> In addition to the basic analyze files, I am adding the nifti-1 flag
>> (magic), and the qform info
>> (quaternion b, c and d and qfac).
>>
>> When I use avwhd to read the header - it does recognize it as a
>> nifti-1 format, but it does not
>> show me any of the additional nifti fields. It (avwhd imagename)
>> actually prints fields that are not
>> in the nifti header file like qform_xorient and sto_xyz (or are
>> they?) Is this expected? Or am I doing
>> something wrong when setting these fields?
>>
>> Here is the output of both 'avwhd testAnalyze.img' and 'avwhd -x
>> testAnalyze.img':
>>
>> thanks!
>>
>> avwhd testAnalyze
>> Byte swapping
>> filename       testAnalyze.hdr
>>
>> sizeof_hdr     348
>> data_type      INT16
>> dim0           3
>> dim1           128
>> dim2           128
>> dim3           23
>> dim4           1
>> dim5           1
>> dim6           1
>> dim7           1
>> vox_units      Unknown
>> time_units     Unknown
>> datatype       4
>> nbyper         2
>> bitpix         16
>> pixdim0        0.0000000000
>> pixdim1        1.5625000000
>> pixdim2        1.5625000000
>> pixdim3        4.0000000000
>> pixdim4        5100.0000000000
>> pixdim5        1.0000000000
>> pixdim6        1.0000000000
>> pixdim7        1.0000000000
>> vox_offset     0
>> cal_max        3607.0000
>> cal_min        0.0000
>> scl_slope      0.000000
>> scl_inter      0.000000
>> phase_dim      0
>> freq_dim       0
>> slice_dim      0
>> slice_name     Unknown
>> slice_code     0
>> slice_start    0
>> slice_end      0
>> slice_duration 0.000000
>> time_offset    0.000000
>> intent         Unknown
>> intent_code    0
>> intent_name
>> intent_p1      0.000000
>> intent_p2      0.000000
>> intent_p3      0.000000
>> qform_name     Unknown
>> qform_code     0
>> qto_xyz:1      1.562500  0.000000  0.000000  0.000000
>> qto_xyz:2      0.000000  1.562500  0.000000  0.000000
>> qto_xyz:3      0.000000  0.000000  4.000000  0.000000
>> qto_xyz:4      0.000000  0.000000  0.000000  1.000000
>> qform_xorient  Left-to-Right
>> qform_yorient  Posterior-to-Anterior
>> qform_zorient  Inferior-to-Superior
>> sform_name     Unknown
>> sform_code     0
>> sto_xyz:1      0.000000  0.000000  0.000000  0.000000
>> sto_xyz:2      0.000000  0.000000  0.000000  0.000000
>> sto_xyz:3      0.000000  0.000000  0.000000  0.000000
>> sto_xyz:4      0.000000  0.000000  0.000000  0.000000
>> sform_xorient  Unknown
>> sform_yorient  Unknown
>> sform_zorient  Unknown
>> file_type      NIFTI-1
>> file_code      2
>> descrip
>> aux_file
>>
>>
>>
>> avwhd -x testAnalyze
>> <nifti_image
>>  nifti_type = 'NIFTI-1'
>>  header_filename = 'testAnalyze.hdr'
>>  image_filename = 'testAnalyze.img'
>>  image_offset = '0'
>>  ndim = '3'
>>  nx = '128'
>>  ny = '128'
>>  nz = '23'
>>  dx = '1.5625'
>>  dy = '1.5625'
>>  dz = '4'
>>  datatype = '4'
>>  datatype_name = 'INT16'
>>  nvox = '376832'
>>  nbyper = '2'
>>  byteorder = 'LSB_FIRST'
>>  cal_min = '0'
>>  cal_max = '3607'
>> />
>>
>>
>
>
Zrinka Bilusic-Vezmar
UCLA Brain Mapping
660 Charles Young Drive South
Los Angeles, CA  90095

310-794-5060
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www.brainmapping.org