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
>
|