No worries! I was wondering if the missing tracts would be available for future use with Tractotron, but I suppose not. Thanks for the reply.
Dear Dr. Chris Foulon,
Thanks for replying to my message.
I did not check the āApply transformation to otherā box during Normalization processing. Is it correct to specify the folder where the lesion data is stored in this part?
Sorry I am not familiar with white matter fiber bundle analysis.
Yes, you should use āApply transformation to otherā (on the lesions folder) when you are normalizing your T1 images if you also need to align your lesions masks to be in the same space as your normalized T1s (if you cannot re-segment the lesions on the normalized T1 which would be better but time consuming).
Normalize, by default, takes T1 images and aligns them to the MNI152 T1 template. Lesion masks are usually binary images, or at least they do not contain the same type of values as in a T1 images (first they do not actually contain a brain). The normalization computes what would be the transformation from your input image to have roughly the same size, shape, and alignment as the template and to do that it needs to find similarities between the input and the template (a brain, the substructures and landmarks). A lesion mask doesnāt have any similarity to the template and thus cannot be directly aligned to the template, that is likely why the disconnectome didnāt work because the lesions you gave it were probably completely wrong (probably outside of the brain).
Dear BCBToolkit Maintainers,
Iām experiencing the same issue with disconnection maps that was mentioned in previous posts. When I try running the disconnection maps using the lesion provided in the package, the software runs for about 2 seconds and then stops, leaving an empty log folder.
Iāve attempted this on several different computers, but I havenāt had any success.
Does anyone have any suggestions for troubleshooting or fixing this problem?
Thanks in advance for your help!
Hella
Hello,
I am still waiting for my new iMac to arrive so that I can test solutions. I thank you for your patience.
Kind regards
Mich
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. Iām 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. Weāre 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,
Iām new here, but I couldnāt 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, Iām 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 āBoost My Disconnectomeā 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 Iād like to ask about: Iām 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. Hereās the log file
logAnacom.txt (2.4 MB)
Could you help me identify what might be causing this? Iād 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 havenāt had time to change the code to fix it yet, sorry.
Itās on my to-do list!
Best,
Chris
Hi Chris,
Thank you for your responseāI really appreciate your time and effort in maintaining the toolkit.
In the meantime, do you have any suggestions for a temporary workaround? Iād 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 havenāt used it myself).
Recently, I also reviewed a few papers using SVR-LSM with the disconnectome, although I didnāt dig too much into the method itself and couldnāt say how robust it is.
Hope that helps!
Cheers,
Chris
Hi Chris,
Thanks for your quick response and for pointing me toward potential alternatives! Iāll try Randomise and SVR-LSM. Also, Iāll 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