Thank you very much.That very reassuring.
Dr Fatemeh Geranmayeh
Wellcome Trust Clinical Research Fellow
The Computational, Cognitive and Clinical Neuroimaging Laboratory
Imperial College London
Telephone : 020 7594 7994
On 13/11/2012 14:31, "Matthew Webster" <[log in to unmask]> wrote:
>Hello Fatemeh,
> Thank you very much for your upload - we have
>looked carefully at the undistorted images and the directionality is the
>same in both cases. The "streaks" in the shift map are only due to a
>change in how we display the shiftmap ( we now display the extrapolated
>map outside the brain rather than the masked version ).
>
>Hope this Helps
>
>Kind Regards
>
>Matthew
>
>> Many thanks Matthew for looking into this problem. Since my first email
>>to
>> you, I
>> have managed to resolve some of my problems with filed map and BBR: The
>> main issue was that FSL 5 needed the non-BETed magnitude image for
>> Unwrapping as well. However I still have 2 concerns as stated below:
>>
>> The UPLOAD REFERENCE is 715510. The file named R1.tar.gz is the FLIRT
>> registration and field map
>> correction with FSL4. The file BBR.tar.gz is the same design.fsf file ,
>> run with FSL5 using BBR and field map correction. The 2 outstanding
>>issues
>> for me are now:
>>
>> 1) why does the 'unwrap shift map,in voxels' ('EF_UD_shift+mag.png'),
>>have
>> streaking outside the brain when unwrapping in FSL 5 compared to FSL4? I
>> have used the same input field maps and magnitude images.
>> 2) The unwrapping direction seams to be different in FSL 5 ( to my
>> untrained eye), even though i use +y for both.
>>
>>
>> Many thanks and best wishes
>> Fatemeh
>>
>>
>>
>> Dr Fatemeh Geranmayeh
>> Wellcome Trust Clinical Research Fellow
>> The Computational, Cognitive and Clinical Neuroimaging Laboratory
>> Imperial College London
>> Telephone : 020 7594 7994
>>
>>
>>
>>
>>
>> On 08/11/2012 15:11, "Matthew Webster" <[log in to unmask]> wrote:
>>
>>> Hello Fatemeh,
>>> Can you tar up your 2 feat directories and upload them
>>> to:
>>>
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>
>>> and let me know the 6-digit reference number?
>>>
>>> Kind Regards
>>>
>>> Matthew
>>>> Dear experts
>>>>
>>>> I loaded a design.fsf file from a previously run analysis in FSL4
>>>>that
>>>> contained field map correction and FLIRT registration into FSL 5. I
>>>>then
>>>> re ran the same first level analysis with FSL 5 and BBR option (not
>>>> making
>>>> any other changes, for example no changes to B0 unwrapping
>>>> option),however
>>>> it appears that the field map correction makes the distortions much
>>>> worse
>>>> when used in FSL 5. (see attached files). I have also attached the
>>>> design.fsf file.
>>>>
>>>> I checked the analysis with a different patient who had less atrophy,
>>>> but
>>>> the problem persists.
>>>>
>>>> Any advise will be much appreciated and I am happy to send more files
>>>> (there was a limit of 200 K on this email)
>>>>
>>>> Many thanks
>>>> Fatemeh
>>>>
>>>>
>>>>
>>>> Dr Fatemeh Geranmayeh
>>>> Wellcome Trust Clinical Research Fellow
>>>> The Computational, Cognitive and Clinical Neuroimaging Laboratory
>>>> Imperial College London
>>>> Telephone : 020 7594 7994
>>>>
>>>>
>>>>
>>>>>
>>>>
>>>> <field map FSL 4.pdf.zip><design.fsf_FSL5.zip><field map _FSL 5
>>>> .pdf.zip>
>>
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