thanks!
zrinka
On Mar 30, 2005, at 12:42 PM, Mark Jenkinson wrote:
> Hi Zrinka,
>
> Glad to help on the qform front.
>
> At the moment we don't actually use the qform in FSL at all (our latest
> release supports most sform support, and *very* limited neurological
> order support).
>
> So in fslview it uses the sform to determine standard space coordinates
> and also the "left-right" orientation (radiological or neurological).
> We
> also display the image in radiological convention, by swapping the
> x-axis when necessary. As for the axes themselves, they are just
> set by the data at present. We don't yet allow viewing in the
> "standard
> coordinate system" (where x-axis would be left-right, y-axis
> anterior-posterior,
> z-axis superior-inferior). However, this is something that we are
> working on. So, for the moment the sform is just used to work out
> the mm coordinates and left-right convention. The qform is ignored
> currently.
>
> Hope this gives you the info you wanted.
> All the best,
> Mark
>
>
>
> On 29 Mar 2005, at 00:16, Zrinka Bilusic wrote:
>
>> 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
>> [log in to unmask]
>> www.brainmapping.org
>
>
Zrinka Bilusic-Vezmar
UCLA Brain Mapping
660 Charles Young Drive South
Los Angeles, CA 90095
310-794-5060
[log in to unmask]
www.brainmapping.org
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