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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