JISCMail - FSL Archives

Dear Jingwen,

at the moment there is no automated option to derive lesions for different lobes.

The main atlases in FSLeyes divide the grey matter in lobes, not really the white matter. There are some white matter atlases, so you can look at them and see if they are useful for your aim.

Alternatively, to create your own mask, please see FSLeyes documentation:

https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/editing_images.html

You can also have a look at this video:

https://www.youtube.com/watch?v=Vaj7BBxqXt0

Hope it helps,

Ludovica

Hi，Ludovica
Thank you very much. Your advice really really helps me a lot.
Another question is about the Volume extraction.
“bianca_cluster_stats <bianca_output_map> <threshold> <min_cluster_size> [<mask>]”
I would like to segment the WMH into specific lobes in the 65~80-year-old elderly, such as temporal lobe, frontal lobe, etc. Should I directly choose the specific mask from the templates supplied in FSL (fsl_atlases ) or create a mask manually? If I need to do the later, how to create it?
Thanks

Jingwen

On 8 Jan 2019, at 7:50 pm, Ludovica Griffanti <[log in to unmask]> wrote:

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.

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1