Thank you very much for this.
I have a few more questions please. Is it valid/possible to use a) field
map correction and/or b) FNIRT in conjunction with lesion masking in
stroke patients?
At the moment I am using field map correction with FNIRT to register older
control brains to standard MNI space. My registration is not great at the
frontal, occipital and temporal poles, resulting in activation a few
millimetres outside the brain in these focal regions. This problem is
particularly worse with my stroke group with left hemisphere lesions,
which I am masking out in the registration. With the patient group I do a
two stage registration: First, I run FLIRT as part of the FEAT cascade;
Second, I updatefeatreg (use the FLIRT to register the T1 to standard
brain with the mask (inverse) as input weighting volume, then concatenate
the transformation matrices, and apply it to the example_func and finally
updatefeatreg).
My first question above (a) is : Is it valid to use field map correction
in stage 1 of the patient registration, before updating the feat reg
folder?
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 24/07/2012 18:04, "Mark Jenkinson" <[log in to unmask]> wrote:
>Hi,
>
>This is going to be in our upcoming release, but in the meantime you can
>find a copy of fsl_prepare_fieldmap at:
> http://www.fmrib.ox.ac.uk/fsldownloads/patches/
>
>This just needs to be copied to $FSLDIR/bin/ on your machine.
>Note that this is only designed to work with Siemens data at present.
>
>All the best,
> Mark
>
>
>On 24 Jul 2012, at 13:57, Fatemeh Geranmayeh wrote:
>
>> Dear Experts.
>>
>> I am following the instructions given at 2012 FSL course on how to
>>process fieldmap phase difference images acquired by Siemens. ( Page 286
>>of the handout). The command fsl_prepare_fieldmap does not work, and I
>>can not get the usage command by just typing it either. I note someone
>>else raised this issue back in May. I have tried both
>>fsl_prepare_fieldmap, and prepare_fieldmap command. There are no manual
>>/help entry for this.
>>
>>
>> Can you help?
>>
>> Best wishes
>> Fatemeh
>>
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