Hi,
You should use the same image with the --fmapmagbrain option in epi_reg.
If the amount of brain that is lost is not very large then it should not significantly affect the registration, as this is only used for initialisation and then refined using the whole head image.
All the best,
Mark
On 14 Aug 2014, at 09:38, Hiroki Kurashige <[log in to unmask]> wrote:
> Hi all,
>
> I have additional question about epi_reg.
>
> I made a brain extracted fieldmap magnitude image to execute the fsl_prepare_fieldmap.
> At the resultant image, as a result to follow the recommendation saying that I should execute brain extraction tightly, some regions of the brain were lost.
> Should I use the same image in --fmapmagbrain option of epi_reg?
> Or, do I need to make another brain extracted imagewhose shape is moreconserved?
>
> Thanks,
> Hiroki
>
> (2014/08/10 21:02), Hiroki Kurashige wrote:
>> Hi Andreas,
>>
>> Thank you very much!
>> Ok, I try to use applywarp.
>>
>> Thanks,
>> Hiroki
>>
>> (2014/08/10 19:36), Andreas Bartsch wrote:
>>> Hi,
>>>
>>>> Is it right?
>>> Yes.
>>>> how should I apply the epi_reg to multiple images
>>>
>>> If I understand you correctly, you may want to take the output of epi_reg
>>> and use applywarp with it.
>>> Cheers,
>>> Andreas
>>>
>>>
>>> Am 10.08.14 10:22 schrieb "Hiroki Kurashige" unter <[log in to unmask]>:
>>>
>>>> Hi Mark,
>>>>
>>>> Thank you for the reply.
>>>> I will try to use epi_reg.
>>>>
>>>> I have several questions about epi_reg.
>>>>
>>>> To make a fieldmap image in rad/s for epi_reg, I think I should do
>>>> fsl_prepare_fieldmap because my data were obtained using
>>>> gre_field_mapping sequence of Siemens scanner.
>>>> I have (two) magnitude data and one so-called presubtracted phase data
>>>> (which may be SPM term).
>>>> I guess that the phase_image in fsl_prepare_fieldmap means presubtracted
>>>> phase data and the magnitude_image means the shorter TE magnitude data.
>>>> Is it right?
>>>>
>>>> Then, how should I apply the epi_reg to multiple images?
>>>> Because my data are motion-corrected fMRI data, I need to apply the same
>>>> registration and de-distortion to multiple images.
>>>>
>>>> Thanks,
>>>> Hiroki
>>>>
>>>> (2014/08/09 19:11), Mark Jenkinson wrote:
>>>>> Hi,
>>>>>
>>>>> Use the epi_reg script (
>>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg ) , as
>>>>> this is what it is designed for.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 8 Aug 2014, at 11:14, Hiroki Kurashige <[log in to unmask]> wrote:
>>>>>
>>>>>> Dear FSL experts,
>>>>>>
>>>>>> I would like to use bbr in flirt.
>>>>>> So, I read the help of flirt and found the options related to bbr,
>>>>>> -wmseg, -wmcoords and -wmnorms.
>>>>>> However, I don't know that how I should set these options.
>>>>>> Could you mind let me know the example of the setting of these options?
>>>>>>
>>>>>> I guess that -wmseg is the white matter nifti file separated from the
>>>>>> others.
>>>>>> But I don't know how I can make it using FSL tool.
>>>>>>
>>>>>> Thanks,
>>>>>> Hiroki
>>>>>
>>>
>>
>>
>> ---
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>
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