Great, that's an easy fix
Thanks!!
------------------------------------------------------------------------
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 15:34
Aan: [log in to unmask]
Onderwerp: Re: [FSL] Black FA map dtifit
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.
>
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.
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