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FSL  August 2018

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Subject:

Re: DTI regestration

From:

Matthew Webster <[log in to unmask]>

Reply-To:

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

Date:

Wed, 8 Aug 2018 16:00:40 +0000

Content-Type:

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Hi Dawn, 
		the -applyisoxfm option in flirt will isotropically resample an image. 
 
Kind Regards 
Matthew 
-------------------------------- 
Dr Matthew Webster 
FMRIB Centre  
John Radcliffe Hospital 
University of Oxford 
 
> On 3 Jul 2018, at 15:53, Dawn Marie Jensen <[log in to unmask]> wrote: 
>  
> Hi Matthew, 
>  
> Thanks for your speedy response!  I hadn’t registered them to T1s at all.  We’re running them in parallel for the pICA analysis. 
>  
> I did run the smoothed DTI images through the FLIRT process and the reran the pICA and that seemed to solve the registration issue.  Is it better to do this before smoothing? 
>  
> I am curious, how would I use flirt to shift the 1x1x1 to 2x2x2? 
>  
> Thank you again, 
>  
> Dawn Jensen 
>  
>> On Jul 3, 2018, at 10:09 AM, Matthew Webster <[log in to unmask]> wrote: 
>>  
>> Hi, 
>>     It’s not clear to me at which point in the pipeline below you are registering the FA images to the T1. However if you’re otherwise happy with the output from TBSS you could isotropically resample to 2mm space with ( e.g. ) flirt. 
>>  
>> Kind Regards 
>> Matthew 
>> -------------------------------- 
>> Dr Matthew Webster 
>> FMRIB Centre  
>> John Radcliffe Hospital 
>> University of Oxford 
>>  
>>> On 2 Jul 2018, at 20:39, Dawn Jensen <[log in to unmask]> wrote: 
>>>  
>>> I'm trying to run a fusion analysis on DTI-FA images and T1.  I'm having trouble with the DTI looking off centered and was wondering if I missed a step in the pre-processing.  Below are the DTI processing steps I've taken so far: 
>>>  
>>> 1)dicom - nii conversion 
>>> 2) eddy correct 
>>> 3) BET extraction 
>>> 4) DTIFIT 
>>> 5) fsl_susan to smooth the FA image 
>>>  
>>> The resultant pICA shows all the DTI data shifted high (partially outside the skull at times, but grouped appropriately) and slightly right of center. 
>>>  
>>> My past experience has only been with TBSS analysis, where the images are registered during the process.  As I understand it, TBSS registers them to a 1x1x1 space, and we'd like to keep the images in 2x2x2.  If there's a way to change that part of TBSS registration, I could use that and then fslsplit the all_FA file.  Should I run flirt instead? 
>>>  
>>> Thanks in advance!! 
>>>  
>>> Dawn Jensen 
>>> Undergraduate Research Assistant 
>>> Brains and Behavior Fellow 
>>> Georgia State University 
>>>  
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