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FSL  November 2007

FSL November 2007

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Subject:

Re: error in dtifit

From:

Swati Rane <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 2 Nov 2007 11:06:31 -0400

Content-Type:

text/plain

Parts/Attachments:

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text/plain (239 lines)

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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