HI - yes, this brain extraction looks fine.
Cheers.
On 26 Jul 2007, at 12:29, Agnieszka Burzynska wrote:
> I uploaded a screenshot of my FA_all (from a tbss tryout on 4 subjects
> only). Number: 563219. Perhaps it helps.
> Best,
> Aga
>
>
> On 26.07.2007 13:19 Uhr, "Steve Smith" <[log in to unmask]> wrote:
>
>> Hi - in general small errors in the BET outline should not be a
>> problem - I would run the full registration process and ascertain
>> that the all_FA images look ok, in which case all is well.
>> Cheers.
>>
>>
>>
>> On 26 Jul 2007, at 12:16, Agnieszka Burzynska wrote:
>>
>>> Dear all,
>>> I am preparing my data for tbss and I believe having a good binary
>>> mask is
>>> crucial for good registration and other steps. After using
>>> default bet
>>> setting from GUI I see that ofen the ventral part of medial
>>> prefrontal
>>> cortex is cut off. If I manipulate with -g and -f from the command
>>> line, I
>>> et it better, but then too much of non-brain voxels are included
>>> (like in
>>> longitudinal fissure or on bottow of the brain).
>>>
>>> Is there any ´gold standard´for bet for dtifit/tbss?
>>>
>>> How the FA maps registration can be affected by too much non-brain
>>> matter?
>>>
>>> Is it recommended to first center my images and use avwroi to cut
>>> the sides
>>> of the image to improve the bet results? Or as long as the mask is
>>> ´roughly
>>> ok´I can be happy with the outcome?
>>>
>>> Thank you,
>>> Aga
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---
>> 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
>> ---------------------------------------------------------------------
>> ---
>> ---
------------------------------------------------------------------------
---
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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