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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