Right, so if you run brain extraction (BET) again and use the new mask in dtifit, it should resolve the problem.
Stam
On 18 Feb 2011, at 14:14, Catherine Delnooz wrote:
> Hi,
>
> The first volume is a non-DW volume in all subjects.
> The brain masks are binary, but in the faulty subjects the intensity is stead as 0.999998 instead of 1.000002.
>
> Catherine
>
> ------------------------------------------------------------------------
> C. C. S. Delnooz , MD
> Resident in neurology
> Department of Neurology (HP 935)
> Radboud University Nijmegen Medical Center
> Donders Institute for Brain, Cognition and Behaviour
> PO Box 9101
> 6500 HB Nijmegen
> The Netherlands
> phone: +31-24-3665094 (UMCN)
> fax: +31-24-3541122 (UMCN)
> Email: [log in to unmask]
>
>
> -----Oorspronkelijk bericht-----
> Van: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Namens Stamatios Sotiropoulos
> Verzonden: vrijdag 18 februari 2011 15:07
> Aan: [log in to unmask]
> Onderwerp: Re: [FSL] Black FA map dtifit
>
> Hi, you can open the images with fslview and check the mask and the data. I would check the mask first, make sure it is 1 everywhere inside the brain. A non-DW volume will have a strong T2-weighted contrast.
>
> Stam
>
> On 18 Feb 2011, at 13:57, Catherine Delnooz wrote:
>
>> Hi Stam,
>>
>> Thanks for your quick reply.
>> What's best way of doing that? I'm quite new in the fsl...
>>
>> Cheers,
>> Catherine
>>
>> ------------------------------------------------------------------------
>> C. C. S. Delnooz , MD
>> Resident in neurology
>> Department of Neurology (HP 935)
>> Radboud University Nijmegen Medical Center
>> Donders Institute for Brain, Cognition and Behaviour
>> PO Box 9101
>> 6500 HB Nijmegen
>> The Netherlands
>> phone: +31-24-3665094 (UMCN)
>> fax: +31-24-3541122 (UMCN)
>> Email: [log in to unmask]
>>
>>
>> -----Oorspronkelijk bericht-----
>> Van: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Namens Stamatios Sotiropoulos
>> Verzonden: vrijdag 18 februari 2011 14:22
>> Aan: [log in to unmask]
>> Onderwerp: Re: [FSL] Black FA map dtifit
>>
>> Hi,
>>
>> Could you please check if your brain masks are binary and whether the bvecs/bvals entries correspond to the appropriate volumes in your data file (i.e. a b=0 entry corresponds to a non-DW volume)?
>>
>> Cheers,
>> Stam
>>
>>
>> On 18 Feb 2011, at 13:02, Catherine Delnooz wrote:
>>
>>> Dear all,
>>>
>>> I'm trying to run dtifit on my data. In about 25% of the subjects I get black .nii outputs from dtifit. The size is about 3kb instead of the 700kb in the good subjects.
>>> I can't find any differences in bvecs/bvals files. A bedpostx_datacheck shows no differences between good and bad results neither.
>>> Does somebody has a clue??
>>>
>>> Best regards,
>>> Catherine
>>>
>>
>>
>>
>> Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
>> The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
>>
>
>
>
> Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
> The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
>
|