Hi - in general we do, in fact recommend using the B=0 image as the
reference, so it sounds like something is odd in your data.
If you'd like to upload it we'll have a look.
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Cheers.
On 10 May 2007, at 17:42, Franck Lamberton wrote:
> Thanks a lot for your response
>
> Jochen Hirsch a écrit :
>> Hi Franck,
>>
>> I haven't found a hint in your e-mail which image volume you
>> specify as
>> reference image.
>>
> I used the following command :
>
> eddy_correct input_colume_4D output_volume_4D 0
>
> So, I use the b0-volume as a reference.
>
> I understand that the high CSF signal can lead to wrong
> corrections. I have already noticed that the external edge of the
> brain in b1000-volumes (and thus, edge of the white matter) are
> moved toward the edge of the CSF in b0-volume (and thus, edge of
> CSF).
> Do you suggest to use another dedicated acquisition, with the same
> parameters as the b0-volume but with an additional pre-inversion in
> order to suppress signal from CSF ?
> Or maybe using the mean volume of all b1000-volumes as a reference...
>
>> But correction for eddy currents distortions will probably fail if
>> you
>> choose the b0-volume due to the high CSF signal which is not
>> present in
>> b1000-images.
>> Regards,
>> Jochen
>>
>>
>>
>>
>>>>> Lamberton Franck <[log in to unmask]> 10.05.07 11.13 Uhr >>>
>>>>>
>> Hi,
>>
>> I worked with DTI a few weeks ago and used FDT in order to compute FA
>> (last
>> version of FSL running on Linux FC4).
>> Recently, I acquired a set of diffusion weigthed images on a subject
>> with
>> minimal head movement (head control) :
>> 40 slices
>> 1 b=0 s/mm2 + 32 different encoding directions at b=1000 s/
>> mm2
>> resolution = 2x2x2 mm3
>>
>> Using the 'Movie mode' of fslview shows that very little distortion
>> occured
>> between successive acquisitions (they seem to be related to
>> eddy-currents).
>> After applying 'eddy_correct', significant geometrical distortion
>> appeared
>> in the se ries that were not present in the first place.
>> I also used avwmaths++ command with the option -Tstd in order to
>> compute
>> the
>> standard deviation of the series. Signifi cant geometrical distortion
>> introduced by eddy_correct induced high std values all arround the
>> brain.
>>
>> I edited the script 'eddy_correct' in order to test different
>> options of
>> FLIRT, cost function (-searchcost) and no ang ular research
>> limitation
>> (-nosearch). In all cases, spurious geometrical distortions remain
>> the same after
>> applying the modified 'eddy_correct'.
>>
>> I also used the option "-interp nearestneighbour" in order to better
>> compare
>> uncorrected and corrected series (less blurring). To do this, I used
>> 'avwmaths++' with '-Tstd' option in order to compute the std
>> volume of
>> only
>> corrected diffusion weighetd volumes. After correction, greater
>> values
>> appear at the periphery of the brain.
>>
>> Does anyone have already seen a similar effect of 'eddy_correct' ?
>> What about using -refweight or -inweight of FLIRT ? How can I use
>> this
>> two
>> options ?
>>
>> Thanks for any response
>>
>> Franck
>>
>>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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