have you tried -Z option in BET?
On 31 Oct 2007, at 14:07, Swati Rane wrote:
> Dear Sir,
>
> I generated the input masks using the following 2 commands:
>
> avwroi data_4D nodif 0 1
> bet nodif nodif_brain -m -f 0.1
>
> data_4D is my 4D data generated using the command 3dto4d.
> I use a lower threshold of 0.1 because my images have low SNR.
> The 4D data is fine, nodif shows all 3 slices but not odif_brain
> and nodif_brain_mask.
>
> Swati
>
> Tim Behrens wrote:
>> How have you generated the input mask? It should be derived from
>> the original data, and therefore have the same number of slices.
>>
>> T
>>
>>
>> On 29 Oct 2007, at 14:08, Swati Rane wrote:
>>
>>> Dear Sir,
>>>
>>> I am not sure if this is what you wanted to know. I checked the
>>> nodif_brain and nodif_brain_mask which indeed have only 2 slices
>>> (nodif has 3 slices). How do I fix that if that is the problem?
>>> I do not know hot to check if the 'littlebit' option is set.
>>> Could you please let me know?
>>>
>>> Thanks!
>>>
>>> Swati
>>>
>>>
>>>
>>> Saad Jbabdi wrote:
>>>> Hi Swati, does it output 3-slice files with the first slice
>>>> empty, or just 2-slice files?
>>>> in the second case, the only way it could happen is:
>>>> - your input mask has only 2 slices
>>>> - you have set the --littlebit option
>>>>
>>>> could you check if one of these two is true?
>>>>
>>>> saad.
>>>>
>>>>
>>>> On 28 Oct 2007, at 21:39, Swati Rane wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> The input to dtifit seems OK. Also I made a mistake. It
>>>>> actually shows the last 2 slice not the first slice i.e. slice
>>>>> no. 1 and 2 but not slice 0.
>>>>>
>>>>> Swati
>>>>>
>>>>> Tim Behrens wrote:
>>>>>> Hi - is it possible that it has processed all three slices,
>>>>>> but when you look at it in fslview, the highest slice number
>>>>>> is 2? If this is the problem, then I think it will be because
>>>>>> fslview starts counting at 0 and not at 1, so slice 2 is
>>>>>> actually the 3rd slice.
>>>>>>
>>>>>> T
>>>>>> On 27 Oct 2007, at 10:56, Steve Smith wrote:
>>>>>>
>>>>>>> Hi - if you look at all timepoints of all slices of the data
>>>>>>> output by eddy_correct do they look ok? I.e., is the input to
>>>>>>> dtifit ok?
>>>>>>>
>>>>>>> Cheers.
>>>>>>>
>>>>>>>
>>>>>>> On 26 Oct 2007, at 17:39, Swati Rane wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I use the older version of FSL (3.3). When I use the dtifit
>>>>>>>> command for my 3
>>>>>>>> slice data, the display says that it has processed all 3
>>>>>>>> slices, but when I
>>>>>>>> look at the FA map in FSL view, I can see only the last 2
>>>>>>>> slices. Can you
>>>>>>>> tell me what is the error in my processing?
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> Swati
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------
>>>>>>> ----------- 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] <mailto:[log in to unmask]> http://
>>>>>>> www.fmrib.ox.ac.uk/~steve
>>>>>>> ----------------------------------------------------------------
>>>>>>> -----------
>>>>>
>>>>>
>>>>> --
>>>>> __________________________________________________________________
>>>>> _
>>>>> Swati D. Rane
>>>>> Ph.D. candidate (Bioengineering) Department of
>>>>> Biomedical Engineering Lab: Yerkes Imaging Center
>>>>> Georgia Institute of Technology Emory University
>>>>> Email: [log in to unmask]
>>>>> <mailto:[log in to unmask]> Phone: 404 712 9109
>>>>>
>>>>> Webpage: http://www.prism.gatech.edu/~gth780f/ <http://
>>>>> www.prism.gatech.edu/%7Egth780f/>
>>>>> __________________________________________________________________
>>>>> _
>>>>
>>>> -------------------------------------------------------------------
>>>> --------
>>>> Saad Jbabdi, Postdoctoral Research Assistant, Oxford University
>>>> FMRIB Centre
>>>>
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222545 (fax 222717)
>>>> [log in to unmask] <mailto:[log in to unmask]> http://
>>>> www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>
>>>> -------------------------------------------------------------------
>>>> --------
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>>
>>> ___________________________________________________________________
>>> Swati D. Rane
>>> Ph.D. candidate (Bioengineering) Lab: Yerkes Imaging Center
>>> Georgia Institute of Technology Emory University
>>> Email: [log in to unmask] Phone: 404 727 5541
>>>
>>> Webpage: http://www.prism.gatech.edu/~gth780f/
>>> ___________________________________________________________________
>
>
> --
>
> ___________________________________________________________________
> Swati D. Rane
> Ph.D. candidate (Bioengineering) Lab: Yerkes Imaging Center
> Georgia Institute of Technology Emory University
> Email: [log in to unmask] Phone: 404 727 5541
>
> Webpage: http://www.prism.gatech.edu/~gth780f/
> ___________________________________________________________________
------------------------------------------------------------------------
---
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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