Dear Jingwen,
please see below
> On 8 Jan 2019, at 3:09 pm, Zhang Jingwen <[log in to unmask]> wrote:
>
> FSL users and experts,
>
> Hello, I'm a user of BIANCA,I have some questions about the userguide.
>
> Q1.about images preparation:
>
> "Choose your base image. This will be your reference space for your input and output images. Register all the other modalities to your base image for each subject."
>
> Can I respectively choose the T1 image as a reference space for each single subject, then register the FLAIR to T1 with FLIRT in fsl?
Yes
>
> "Perform brain extraction on (at least) one modality to be able to derive a brain mask."
> Does the "brain extraction" refer to remove the skull?
Yes, the FSL tool that dose it is BET (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET)
> Q2.about Master file preparation
>
> How to create the master file? by manually editing in a new text file or inputting the command lines in terminal?
you need to create a .txt file
>
> Q3.“--singlefile=<masterfile> name of the master file (e.g. masterfile.txt)”
>
> What should I type in the option “Masterfile”? the file name(e.g. masterfile.txt) or the entire path to the text file?
If you type masterfile.txt it will only work if you are calling BIANCA from the directory containing masterfile.txt. If you use the full path it will work regardless the working directory you are in when calling BIANCA.
Hope it helps,
Ludovica
>
> I really appreciate for your kind help.
>
> Best wishes.
>
> Jingwen.
>
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