Thank you very much Mark.
Best wishes
Fatemeh
On 04/08/2012 09:04, "Mark Jenkinson" <[log in to unmask]> wrote:
>Dear Fatemeh,
>
>It is possible to use fieldmaps with lesion masks and we would encourage
>it.
>The difficulty is checking that all the intermediate registrations are
>fine.
>There are a few things you should check:
> - that the fieldmap does not contain any artefact in the lesion areas
> - that the registration of the fieldmap magnitude to the example_func
>looks OK
> - that the example_func to structural registration looks OK
>Assuming that these are OK (and ideally these should be fine with lesions
>as
>the lesions will be present in all images of that subject) then the
>strategy you
>propose (using the lesion mask for the structural to standard
>registration)
>should work fine.
>
>All the best,
> Mark
>
>
>
>
>
>
>On 1 Aug 2012, at 12:57, Geranmayeh, Fatemeh wrote:
>
>> 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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