BCBToolkit Questions

186

Hi Chris and Michel,

I’m trying to use the normalisation feature of BCBtoolkit to normalise my lesion mask. The output of the enantiomorphic and normalised T1 file seemed alright, but the lesion masks had this weird white edge outside the skull alongside the lesion (using fsleyes the value of this white edge is 1.0). Unfortunately I can’t upload any attachment as a new user. Do you have any idea why this may be the case and how may I resolve this?

Thanks a lot!
Shangqi

187

Hi Shangqi,

Yes I know that issue with the enantiomorphic.
You can maybe just use a brain mask to get rid of this white ribbon?

Let me know if you succeed.
cheers

mich

188

Hi Michel,

Thank you for the quick response. The mask worked for me! I was worried before that the lesion mask might be problematic as well, but I suppose the only issue was with the white ribbons. Thanks for the help!

Best,
Shangqi

189

Hi BCBToolkit Team,

I installed BCBToolkit and found out that the BCBToolkit.sh needs the write permission to the config file. I wonder if we could copy the config file to somewhere else (Home directory, not the system) and specify the path / redirect the command to write to that config file instead?
We want to prevent users write the files in the system.

Thanks in advance for your help.
Angel

190

Hi Angelika,

The GUI handles the config file, so I’d need to recompile the whole package just to make that change. But you could just put the file in the Tools/extraFiles folder of the BCBtoolkit so it doesn’t need to be created. The BCBToolkit will, however, require writing permissions in the tmp folder inside the BCBtoolkit folder. You would need to change the path of the $tmp variable in the bash scripts of Tools/scripts to another tmp location.

You can use this blank configuration file after removing the “.txt” extension:
BCBToolKit.conf.txt (1.3 KB)

Hope that helps,
Chris

191

Hello BCBToolKit administrators.
I would like to know something about Normalisation.
I heard that ANTs can convert FLAIR images to MNI templates with non-linearregistration.
Since the Normalisation process in BCBToolKit uses ANTs in the background, if I set the template file to a MNI FLAIR image (FLAIR templates | Brainder.), can I convert the FLAIR image and the Lesion data mapped in it to MNI?

192

Hi Shun,

I never tried this but i’d be curious to know if it works. Cheers. mich