Dear Mich,
Thank you for taking the time to explore potential solutions. Could you provide an estimate of when you anticipate being able to test them?
Kind regards,
Hella
Dear Hella,
I finally received an M4 iMac. I’m afraid we understood where the problem is coming from.
Apple changed the structure of the processor that now require us to compile a specific version of BCBtoolkit for apple M3 and M4. While this is possible in principle we are actually struggling with one binary (track_vis) that we cannot make work at the moment. We’re working on a solution. thanks for your patience. Meanwhile BCBtoolkit still works on M1 and Intel processors as well as linux. Kind regards. mich
I am pleased to let you know that we found a solution.
We will update the website in next days with a new build that works with M4.
Thanks for your patience.
michel
Hello,
I’m new here, but I couldn’t seem to find anything about this in previous posts so here goes:
I have quite a bit of data, so running the disconnectome maps with the boosted connector takes a (very) long time. Is it possible so somehow batch process the use of the BCBToolKit or to otherwise parallelize it? Specifically the disconnectome maps?
Kind regards,
Mads
Hello disconnectome map is parallelised, I personally ran 2666 lesions in 2020 and I remember it took a couple of days (Brain disconnections link structural connectivity with function and behaviour | Nature Communications)
The code of the app is opened so feel free to explore way to optimise it and thanks for letting us know if you find a way 
As for M4 version of bcbtoolkit, I’m running tests but it should be available soon.
Cheers
Mich
1 Like
Ok the update M3-M4 is done. We also upgraded the normalisation (for intel processor as well)
Here is the procedure to install on M3-M4 let me know if it works.
Apologies for the delay.
M3-M4 MACS
Download BCBtoolkitM3M4 Dropbox
Install java https://adoptium.net/
Install FSL FSL - the FMRIB Software Library
Remove the permission issue
sudo xattr -dr com.apple.quarantine [application path]
Dear All,
I am interested in expanding the dataset used for DISCONNECTOME MAPS beyond the 10 healthy controls (Thiebaut de Schotten et al., 2017). I came across a reference to the “Boost My Disconnectome” section for downloading a preprocessed data package that includes up to 35 participants, but I could not locate this option. Could you please provide guidance on how to access and use this data package?
Additionally, I would like to know if it is possible to use my own healthy control dataset for this analysis instead of the default dataset. If so, could you explain how to integrate my custom data into the process?
Looking forward to your response.
Best regards,
Xinye Wu
Hi Xinye,
Yes you can boost your disconnectome by downloading the extra connectomes on www.bcblab.com (section open data).
You just have to add those or replace what is in BCBToolKitOSX/Tools/extraFiles/tracks
cheers
mich
Thank you, Mich, I understand now. Also, besides the data provided in the open data, can I use my local healthy control samples as a replacement?
Yes you can! But note that our processing was optimised for the most anatomically accurate tractography
cheers
mich
Got it, thanks!
I have another issue I’d like to ask about: I’m using the AnaCOM2 feature of BCBtoolkit to calculate structural disconnection related to clinical scales, following the approach described in your paper, with 50 Disconnectome Maps as lesions. However, after running the program for several minutes, it keeps generating cluster413.nii.gz in the Results directory/anacomClustersDir/ without making any progress. This issue persists for one or two days with no further developments. Here’s the log file
logAnacom.txt (2.4 MB)
Could you help me identify what might be causing this? I’d really appreciate your advice.
Best wishes.
Xinye
Hi Xinye,
Sorry, this is a known bug with some values that can cause an infinite loop. I haven’t had time to change the code to fix it yet, sorry.
It’s on my to-do list!
Best,
Chris
Hi Chris,
Thank you for your response—I really appreciate your time and effort in maintaining the toolkit.
In the meantime, do you have any suggestions for a temporary workaround? I’d be happy to try any potential fixes on my end.
Best,
Xinye
Hi Xinye,
There are several papers that used the Randomise tool from FSL with the disconnectome maps, and they even have a cluster-based option, I believe (I haven’t used it myself).
Recently, I also reviewed a few papers using SVR-LSM with the disconnectome, although I didn’t dig too much into the method itself and couldn’t say how robust it is.
Hope that helps!
Cheers,
Chris
Hi Chris,
Thanks for your quick response and for pointing me toward potential alternatives! I’ll try Randomise and SVR-LSM. Also, I’ll keep an eye out for any updates on the bug fix and look forward to the solution when you have time to address it.
Best,
Xinye
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
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
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
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
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