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FSL  February 2011

FSL February 2011

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Subject:

Re: Black FA map dtifit

From:

Stamatios Sotiropoulos <[log in to unmask]>

Reply-To:

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

Date:

Fri, 18 Feb 2011 14:06:55 +0000

Content-Type:

text/plain

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text/plain (60 lines)

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.
> 

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