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/
___________________________________________________________________
|