Dear Joerg,
You are right that this information is missing from the possum output.
Your solution looks fine, although you can also use fslcpgeom to set/copy useful header information from an existing image.
We will fix this output from possum in a future release.
All the best,
Mark
On 30 Apr 2014, at 13:10, Joerg Pfannmoeller <[log in to unmask]> wrote:
> Allright, just to finish this:
>
> Important informations can be found on the web page: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
>
> The following commands did the job for me:
>
> fslswapdim image_homo.nii.gz x -z -y image_homo02.nii.gz
> mri_convert --in_orientation LIP --out_orientation LIP image_homo02.nii.gz f.nii.gz
>
> The options are set in order to generate an image with the orintation needed for freesurfer.
>
>
>
>> Dear Experts,
>>
>> I have a problem with the output of Possum. After a succesfull simulation I recognized that some information in the header of the file seem to be missing. If I use mri_info I get the following output:
>>
>> mri_info image_homo.nii.gz
>> WARNING: neither NIfTI-1 qform or sform are valid
>> WARNING: your volume will probably be incorrectly oriented
>> Volume information for image_homo.nii.gz
>> type: nii
>> dimensions: 128 x 17 x 120 x 108
>> voxel sizes: 1.4922, 2.0000, 1.4929
>> type: FLOAT (3)
>> fov: 191.000
>> dof: 0
>> xstart: -95.5, xend: 95.5
>> ystart: -17.0, yend: 17.0
>> zstart: -89.6, zend: 89.6
>> TR: 2040.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
>> nframes: 108
>> PhEncDir: UNKNOWN
>> ras xform not present
>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 95.5000
>> : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.0000
>> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 89.5755
>> Orientation : ???
>> Primary Slice Direction: unknown
>>
>> voxel to ras transform:
>> -1.4922 0.0000 0.0000 191.0000
>> 0.0000 2.0000 0.0000 0.0000
>> 0.0000 0.0000 1.4929 0.0000
>> 0.0000 0.0000 0.0000 1.0000
>>
>> voxel-to-ras determinant -4.45545
>>
>> ras to voxel transform:
>> -0.6702 0.0000 0.0000 128.0000
>> -0.0000 0.5000 -0.0000 -0.0000
>> -0.0000 -0.0000 0.6698 -0.0000
>> 0.0000 0.0000 0.0000 1.0000
>>
>>
>> There is a problem with the qform and the image orientation. Which ibformation do I have to add and how can I add the information?
>>
>> So long pfannmoe
>
>
> --
> Joerg Pfannmoeller <[log in to unmask]>
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