BCBToolkit Questions

207

Dear Annibale,

By configuration I mean what type of computer (e.g. apple MacBook Pro M1)
By directory I mean the name of the folder where BCBtookit is in and the folder before that and all folder before that until you can’t name it :slight_smile: (e.g. /Applications/BCBToolKitOSX)

cheers
mich

208

Dear Mich,
Thank you very much for your prompt reply, and please excuse my lack of knowledge—I am approaching this field from a background quite distant from computer science (as you have surely noticed :smile:). Indeed, it is an Apple M1 Pro! Please find below the file path:

/Users/annibaleantonioni/Downloads/BCBToolKitOSX

Many thanks again for your help and availability!
Best,
Annibale

209

Hi Mich, I am studying my bachelors on psychological sciences and I’ve started to learn about lesion mapping. That’s why I wanted to learn how to use the bcbtoolkit. What would you reccomend to an absolute beginner? Are there any tutorials explaining how to work on it?

Thank you,
Sude

210

It’s pretty much self explanatory in the useguide http://www.bcblab.com. Although we’ve been having some compatibility issues on the new macs. let me know. mich

211

Hi Annibale,

Sorry did you manage to fix your issue?
cheers

mich

212

Dear BCB-team,

We’re conducting a study trying to create disconnectome maps to correlate with a behavioral outcome. In a previous post (BCBToolkit Questions - #11 by BCB_LAB), I read that when the number of participants is higher than 50, it was suggested to use FSL’s Randomise instead of Anacom2. We’ve merged the individual disconnectome maps with FSL merge and then used the resulting 4D-NIFTI file as a dependent variable in the Randomise GLM. Does this seem reasonable and is this the correct way of using Randomise in this instance? Just wanting to make sure that we are doing it correctly.

Also, are there any quality assessments recommended for the BCB-disconnectome output?

Kind regards,

Carl

213

Dear BCBToolkit Maintainers,

I’m 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. My operation system is Ubuntu20.04. How should I do to solve this issue?

I am looking forward to your reply!

Kind regards,
Candy

214

Hi Candy,

Do you have any message in the terminal? Is there no pop-up window when it “finishes” with messages?

The BCBToolkit folder does not contain any space or special characters?

Best,
Chris

215

Dear Dr Foulon,

Thank you very much for your response. After I changed the output directory so that it is no longer the same as the lesion folder, the software runs normally. It’s great to see it working now. Many thanks again for your help.

Best regards,
Candy

216

Hi everyone !
I want to use the Disconnectome Maps from the BVB ToolKit.
I’ve uploaded the files from Disconnectome Package 1.
Replace them in the extraFile folder.
However the simulation crashes just few seconds after I ran it.

Thanks a lot for your help !
Pierre-Olivier

217

Hi Pierre-Olivier.

We’re running into some issue with Mac M3 M4 M5 that we solved using the following trick https://storage.googleapis.com/bcblabweb/download/readme.txt. If this doesn’t make it can you let me know the specifications of your computer? Meanwhile I should acquire an M5 as soon as the mac book air M5 is out.
cheers

mich

218

Hi everyone!

With @Pierre-Olivier_Moser we have tested a solution for the mysterious issue on MacOSX that was not showing errors anywhere but preventing the Disconnectome Maps module from doing anything (clicking on “Run” ends immidiately without output).

Replace BCBToolkitOSX/Tools/scripts/xargs_disco.sh with BCBToolKit/Tools/scripts/xargs_disco.sh at master · chrisfoulon/BCBToolKit · GitHub and that should fix a potential incompatibility on Mac.

Also, some issues might arise from incompatibilities with the track_vis binaries on some versions of mac, apparently there is a tool from Apple called Rosetta that fixes compatibility issues on newer mac versions.

I hope this helps!
Chris

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219

Thank you very much for your support & your quick answer !

Pierre-Olivier

220

Thank you for developing and providing the BCBToolkit!

I have been running the toolkit successfully in WSL2 with MRI lesion data derived from 3T T1-weighted data from 40 participants with stroke.

I am interested in the ‘Open Data’ DISCONNECTOME Packages. I understand these to be a way to enhance the performance of the ‘Disconnectome Maps’ tool (which has worked great using the default installation 10 participants) and that these additional healthy control participants can be added to the ‘BCBToolKit\Tools\extraFiles\tracks’ directory. The BCBLab website includes four different packages: 1, 2, and X (1mm and 2mm). How can I determine which of these packages represents the most appropriate enhancement for my case? Do you happen to have information regarding how much computation time will increase with the additional healthy control data as well as how much additional variance in the data is accounted for by adding N more healthy control participants?

Thank you in advance for your assistance,
Nate

221

Good question. We added more subject to satisfy reviewers but honestly 10 are enough to get a good grasp of the average disconnection in your patients. You’ll find the demonstration in Foulon et al. Gigascience 2018 suplementary material if i remember well (happy to be corrected here). Having said that, the best so far is the package X 1mm (if your lesions are at 1mm). Adding these subjects will significantly increasing the disconnectome processing time (roughly x18 time as there is 18 times more subjects)

1 Like