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
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?
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.
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?
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
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.
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!
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.
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.
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?
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!
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.
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)
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?
