Dear Sir,
bet2 worked!
Thanks!
Swati
Matt Glasser wrote:
> 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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