You might need to use bet2 (which is now the regular bet in FSL 4.0).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Swati Rane
Sent: Wednesday, October 31, 2007 11:35 AM
To: [log in to unmask]
Subject: Re: [FSL] error in dtifit
Dear Sir,
I could not find the -z option in the BET options. Am I missing
something here?
(I am using FSL 3.3)
Swati
Steve Smith wrote:
> 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
>
---------------------------------------------------------------------------
>
--
___________________________________________________________________
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/
___________________________________________________________________
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