Hi,
Sorry about the delay - just got back from ISMRM.
Your file has not actually got a valid qform set.
If you look at the qform_name it is "Unknown".
When both the qform and the sform are Unknown, as in
this case, the contents of the qform and sform matrices
are ignored and a default "radiological" matrix is used
instead. The default matrix will have a negative value
for the 1st diagonal element and positive for the other
diagonal elements.
So your images are all being interpretted the same as
in the Analyze case (which also uses the default "radiological"
setting). This is why Feat works correctly and gives you
correct left-right activations.
Note that converting from Analyze to nifti using avwchfiletype
(or any other fsl utility) will set the qform and sform to Unknown
(unless a non-zero origin is set in the Analyze file) and will
therefore keep a "radiological" orientation. As long as you
continue to convert the images like this then things should be
OK.
Hope this answers your questions.
All the best,
Mark
On 9 May 2006, at 17:24, Vishwadeep Ahluwalia wrote:
> Hi,
> Sorry to send another orientation question. I ve 241 functional
> time series images in the analyze
> format that i convert to nifti using avwmerge. i ran avwhd on the
> nifti file and it gave me the
> following output...
> filename erpspiral.nii.gz
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 64
> dim2 64
> dim3 25
> dim4 241
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 3.7500000000
> pixdim2 3.7500000000
> pixdim3 4.0000000000
> pixdim4 1.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> 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 3.750000 0.000000 0.000000 0.000000
> qto_xyz:2 0.000000 3.750000 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 1
> descrip FSL3.3
> aux_file
>
> running avworient -getorient gives me Radiological. i also ve
> structural dicom data that i
> converted to analyze using SPM5 and then to nifti using
> avwchfiletype. running avwhd on that
> gives me qform orientation and sform as Right - left and avworient
> -getorient gives me
> radiological.
> Why does avworient -getorient output show both as radiological
> while their qformorient entries
> are opposite?
> and considering that my functional images are L-R ,P-A ,I-S ; how
> does FEAT show the output
> correctly (since i do get right hemispheric activation for left
> finger tapping) considering that my
> functional data has a different qformorient than both the
> structural and standard?
>
> I read previous posts on orientation issues but couldnt find one
> that had unknown sform issue
> mixed in. any help would be appreciated.
>
> regards,
>
> Vishwadeep A.
> Grad. Student
> Medical Physics Program
> VCU
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