Hi Jesper,
we are running some sample data through the FSL pipeline for distortion correction and have a few questions.
We ran top-up on our b=0 images and wanted to feed the results to eddy, but we don't have a guide on the FSL website yet. Could you please send an example of the command line? I assume something like:
eddy --imain=DWIseries --mask=brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=topup_output --out=eddy_out

We have also acquired phase-up and down for all the diffusion volumes we have. What is your experience on this point? Is it better to run top-up on each individual image or to just apply the b=0 warp? Any detail on this issue would be useful.

Finally, does eddy rotate the b-matrix according to the movement of the head?

Stefano Marenco, MD
NIMH/CBDB
10 Center Drive, Bldg 10 room 3C103
Bethesda MD 20892
Tel 301 435-8964
Fax 301 480-7795
Email: [log in to unmask]

-----Original Message-----
From: Sarlls, Joelle (NIH/NINDS) [E]
Sent: Tuesday, October 23, 2012 11:38 AM
To: Marenco, Stefano (NIH/NIMH) [E]
Subject: Re: FSL TopUp now officially supported

Hi Stefano,
It looks like the topup finished running last night and I was successfully able to apply the results to correct the images. However, I went to read through the documentation on how to feed the results into the 'eddy' software and there is NO information on their webpage about how to run the code. They don't even have an example command line for me to try to work from. Do you have any idea how to run 'eddy'? I see from the parameter list that there is a flag for feeding in the topup results. Alternatively, we could run the data through 'eddy_correct' and then run the topup. Let me know what you think.

Thanks, Joelle



On Oct 22, 2012, at 1:51 PM, Marenco, Stefano (NIH/NIMH) [E] wrote:

> I will come by around 4:30 pm... but will not be able to stay after
> 5:30 pm
>
> Stefano Marenco, MD
> NIMH/CBDB
> 10 Center Drive, Bldg 10 room 3C103
> Bethesda MD 20892
> Tel 301 435-8964
> Fax 301 480-7795
> Email: [log in to unmask]
>
>
> -----Original Message-----
> From: Sarlls, Joelle (NIH/NINDS) [E]
> Sent: Monday, October 22, 2012 1:47 PM
> To: Marenco, Stefano (NIH/NIMH) [E]
> Subject: Re: FSL TopUp now officially supported
>
> Hey Stefano,
> I went ahead and installed a local copy of FSL version 5. I have a volunteer to scan today from 2-4pm, but if you're available around 4:30pm then maybe we can try to get a data set running with the new TopUp. Alternatively, I'm available anytime tomorrow.
>
> Thanks, Joelle
>
>
> On Sep 26, 2012, at 10:14 AM, Marenco, Stefano (NIH/NIMH) [E] wrote:
>
>> Here is a thread from the FSL mail list. They have released version 5, which includes support for Top_up and eddy (a new eddy correction program) (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/WhatsNew ).
>>
>> A more detailed description of what Topup does can be found here:
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide
>>
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide
>>
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApp
>> l
>> ytopup
>>
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupFurtherInformat
>> i
>> on
>>
>> as you can see from Jesper's response below, "eddy" can take advantage of topup, combining the two corrections.
>>
>> Joelle or Souheil, are our data acquired on a sphere or a half-sphere?
>>
>>
>> Stefano Marenco, MD
>> NIMH/CBDB
>> 10 Center Drive, Bldg 10 room 3C103
>> Bethesda MD 20892
>> Tel 301 435-8964
>> Fax 301 480-7795
>> Email: [log in to unmask]
>>
>> -----Original Message-----
>> From: Jesper Andersson [mailto:[log in to unmask]]
>> Sent: Wednesday, September 26, 2012 4:32 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] TopUp --datain
>>
>> Hi again,
>>
>>> Hi Jesper
>>> OK perfect this is what I collected (opposing phase encode + fieldmap).
>>
>> actually the opposing phase encode is "instead of" a fieldmap (the data with the opposing PE is used to estimate something that is quite similar to a fieldmap). However I am happy that people use both suspenders and a belt until they know how well topup works for them.
>>
>>> Does it also mean that other dataset have to be processed with standard Eddy Current Distortion and not TopUp?
>>
>> topup is not intended for correcting for eddy current distortions. For that you can use either the old eddy_correct or the new tool called eddy. The latter does not require opposed blip data, but will take advantage of it if it is available. It is very much a beta release (maybe even alpha), but we have had some very encouraging results with it so we hope that as we iron out the wrinkles it will become the method of choice for the future.
>>
>> Jesper
>>
>>
>>>
>>> Thanks,
>>>
>>> michel
>>>
>>>
>>>
>>> On 26 Sep 2012, at 08:57, Jesper Andersson wrote:
>>>
>>>> Hi Michel,
>>>>
>>>> as a little addendum to Saads reply I should stress that topup can only be used if the data was acquired in a way that allows it. I.e. if data was for example acquired twice with opposing phase-encode blips. Data that was acquired without planning to use topup is unlikely to be possible to process with topup.
>>>>
>>>> This is equivalent to other types of distortion correction where if for example one has not acquired fieldmaps one cannot use fieldmap based corrections.
>>>>
>>>> Good luck Jesper
>>>>
>>>>
>>>> On 26 Sep 2012, at 09:49, Michel Thiebaut de Schotten wrote:
>>>>
>>>>> Dear experts,
>>>>>
>>>>> This morning I tried to run topup for the first time, to correct distortion on a DWI dataset.
>>>>> Following the help menu I wrote the following command
>>>>>
>>>>> topup --imain=DWI.nii --datain=bvecs
>>>>>
>>>>> But the following error occurred:
>>>>> TopupFileIO:: msg=TopupDatafileReader:: error reading file bvecs
>>>>> What is supposed to be the --datain if not the Bvec?
>>>>>
>>>>> Thanks for your help an the new release of FSL, Kind regards,
>>>>>
>>>>> Michel
>>>>>
>>>
>