Hello Dr Smith,
Thank you for your reply. I have tried your suggestion and the results are
much better since the orientation is no longer swapped. I did not realize
that using the NEUROLOGICAL convention would be such a problem for FAST, but
using the RADIOLOGICAL convention seems to do the job as you had suggested.
Thank you again for your time. Happy holidays!
Best Regards,
On Tsang
===
On Fri, 7 Dec 2007 10:17:21 +0000, Steve Smith <[log in to unmask]> wrote:
>Hi - yes, this is still related to the NEUROLOGICAL convention you are
>using in these Brainweb-derived files, which is a problem for FAST and
>many other NIFTI-reading programs at this point. If you run:
>
>fslswapdim t1_pn3_rf20_ns -x y z fixed
>fslorient -swaporient fixed
>fast -e -ov -os fixed
>
>You get a very nice segmentation. Otherwise the FAST output is L-R
>swapped relative to the input, which would explain your poor overlap
>measures.
>
>Cheers.
>
>
>
>
>On 6 Dec 2007, at 16:24, On Tsang wrote:
>
>> for archival purposes:
>>
>> Dear Steve,
>>
>> Thank you for your offer to help. The file I am attaching is the skull
>> stripped Brainweb T1-w phantom and I just used the default FAST
>> settings by
>> calling 'fast filename.nii'. From the output image, I extract the
>> different
>> tissue classes. Thank you again for your time.
>>
>> Best,
>> On Tsang
>
>
>---------------------------------------------------------------------------
>Stephen M. Smith, Professor of Biomedical Engineering
>Associate Director, Oxford University FMRIB Centre
>
>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>+44 (0) 1865 222726 (fax 222717)
>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>---------------------------------------------------------------------------
>=========================================================================
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