Thanks very much!
We will give it a try.
On Dec 23, 2005, at 4:50 PM, Stephen Smith wrote:
> Hi - this is just because you have a very large FOV in Z - you can
> either
> just cut down the FOV before running BET or set the centre for BET:
> bet test grot -c 136 190 76
> This then works fine.
> Cheers, Steve.
>
> On Fri, 23 Dec 2005, Lipton, Michael wrote:
>
>> Thanks, the file is holidays.tar.gz
>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf
>>> Of Stephen Smith
>>> Sent: Friday, December 23, 2005 1:07 PM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] Incomplete mask
>>>
>>>> 1. Is there a way to get BET to truly mask out ALL of the non-brain
>>>> tissue?
>>>
>>> Impossible to know without seeing an example - if you want to upload
>> an
>>> example we can have a quick look:
>>>
>>> Please upload the files in a single compressed tarfile to
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>> and then email me the upload ID.
>>>
>>>> 2. If I am forced to make edits using FSLView, is there a way to
>>>> only manually draw ROIs on a portion of the slices (every other,
>> every
>>>> third, etc.) and have the program interpolate and join these
>>>> discontinuous ROIs into a single mask? This could significantly cut
>> the
>>>> time required to mask out images.
>>>
>>> Sure - you could use some combination of downsampling, editing and
>> then
>>> re-upsampling (using flirt) or else maybe the morphology options in
>>> avwmaths to fill in between slices.
>>>
>>> Cheers, Steve.
>>>
>>>>
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>>
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>
>
> --
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, John Radcliffe 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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