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

193

Hello,

I’m experiencing a similar issue with disconnectome maps that was mentioned in previous posts discussing the M3/M4 version. When I try running the disconnectome maps, the software runs for a few seconds and then stops, leaving an empty log folder. I don’t receive an error message. I’m running on M1 macbook air, but I’ve attempted this on a few computers. I was able to run tractotron but I haven’t had any success with the disconnectome maps. I’ve verified all my lesions are binary MNI152 nifti format and the directories are correct. Could you please help me resolve this issue?

Thank you!

194

Dear HDR,

Did you try the fix for M3/M4 we provide on the http://www.bcblab.com website?
cheers

mich

195

Hi Mich, Yes - the M3/M4 fix solved my tractotron issue but not the disconnectome maps.

196

Are there any additional fixes you could suggest for generating the disconnectome maps? Thank you!

197

Just to be sure did you do all the follwowing?

  1. Download BCBtoolkitM3M4 https://www.dropbox.com/scl/fi/9yh4ss6gojat456wkren1/BCBToolKitOSXM3M4.zip?rlkey=hbezfb7w95tzczkorjz8fp911&dl=1

  2. Install java https://adoptium.net/

  3. Install FSL FSL - the FMRIB Software Library

  4. Remove the permission issue in the terminal
    sudo xattr -dr com.apple.quarantine [BCBtoolkit application path]

198

Yes, and I’ve uninstalled and reinstalled these all to double check the versions are correct

199

Hi Mich,

Based on your previous reply, you mentioned that besides the data provided in the open data, I could use my local healthy control samples as a replacement, but you also pointed out that your processing was optimized for the most anatomically accurate data.

I would like to conduct a comparative study using my local healthy control samples alongside the data available on your website (www.bcblab.com, section “open data”) from the “DISCONNECTOME Package X (180 additional subjects HCP7T 1mm) – Savalaggio et al. Brain 2021” to investigate if there are any potential differences in the results.

Therefore, replicating your methodology with my local healthy control samples is crucial for my analysis, but I’m having difficulty locating the specific processing steps through the keyword “Savalaggio et al. Brain 2021.” Could you kindly provide more detailed information on the processing workflow?

Thank you in advance!

Best,
Xinye

200

Apologies for the delay. That is strange indeed M1 is not an issue usually. You can send me your lesions to michel.thiebaut@gmail.com I’ll process it for you. Sorry about this. cheers

mich

201

Hi Xinye,

Sorry for this misunderstanding “DISCONNECTOME Package X (180 additional subjects HCP7T 1mm) – is the corresponding dataset used in Savalaggio et al. Brain 2021. You should find all the details regarding the preprocessing in the supplementary material of Thiebaut de Schotten et al. natcomms 2020 Brain disconnections link structural connectivity with function and behaviour | Nature Communications
I’ll be away in august but feel free to shoot a question here if you run in any additional struggle (this processing is not easy).
Cheers

mich