So, yes the images have to be in the same space as the tractographies used.
For the images not showing anything in the output, like that I can see a couple of explanations. If your lesions are outside of the tractographies there won’t be any fibre crossing the lesions. It can happen with erroneous registration, or maybe some lesions that are at the very surface of the cortex or small lesions outside of what’s tracked with the tractography.
If you can send me a couple of lesion masks that did not work and I can have a look if you want.
Concerning the non-binary masks, it could potentially be a problem if the values are between 0 and 1 or even negative, I haven’t tested it but, I am guessing track_vis is taking all the voxels above 1 internally. That’s why we usually advise users to binarize the masks.
Hi Chris,
I am trying to do disconnectome mapping on a Linux Ubuntu platform and have the same problem as Max.
Data is supposedly properly written (but it only takes a sec, so probably nothing was computed… )
The log file is empty.
Has there been a fix for this for linux machines?
Best regards,
Julian
Hi Julian,
Sorry you’re having issues with the BCBtoolkit.
What version of Ubuntu are you using?
Have you checked the permissions of the BCBtoolkit folder? You can do it by using ”cd” into the parent folder of the BCBtoolkit and then use ”ls -l BCBToolkit”
You can try
”chmod -R 775 BCBToolkit” to change the permissions of the bcbtoolkit folder.
thanks for the quick reply. To make matters more complicated, I created a Linux workspace with WSL2 on my Windows 10 machine. Ubuntu is version 2004.20221.825.0.
Oh I never tried with wsl2. It’s still from a windows machine so I guess there could be different things going on in the background. Have you been able to install FSL and run its commands normally?
The BCBtoolkit is using fsl’s binaries contained in the package
Hey Chris,
so, after some tears I reestablished everything from scratch. I used Ubuntu 18.04 now and reinstalled fsl. With the newer version of ubuntu fsl was not running properly somehow. Now everything is running smoothly.
thanks for your help!
Best regards,
Julian
I apologize for asking such a basic question but I’m having issues running the BCBToolKit.command script on my MBP (OS 11.6). My understanding is java is deprecated/is incompatible with newer mac operating systems. Is there a software version that is compatible with Big Sur or do I need to use a machine with an older OS if I want to use the BCB toolkit?
Hello and thanks for your help. I removed the comment because I thought I had found a solution but it turns out I have the same issue. When I try to run the BCBToolKit.command file I get the following error…
Unable to load native library: dlopen(/path/local/to/my/computer/Downloads/BCBToolKitOSX/jre/lib/libjava.dylib, 1): Library not loaded: @rpath/libverify.dylib
Referenced from: /path/local/to/my/computer/Downloads/BCBToolKitOSX/jre/lib/libjava.dylib
Reason: image not found
I thought it could have been a java issue so I downloaded a recent version but that did not fix the issue.
I also ran ‘sudo spctl --master-disable’ and this did not solve the problem.
Any suggestions you have would be much appreciated.
Hi Frank, I’ve been there. The new macOS block some of our files. So for the first 10 launch, you will have to allow them manually until we find a solution.
Let me help you with this process.
In system preferences, you need to go in security & privacy, under the general tab you will be able to allow the files that are blocked one by one.
This will require you to restart BCBtoolkit a few times (about 10) but it will work in the end and you won’t have to do this process ever again. Sorry for your trouble we’re looking into finding an easier fix at the moment. Kind regards. Mich
However, after installing java the BCBToolKit.command kept throwing me the same error.
I then re-downloaded the BCBToolKitOSX.zip folder and ran BCBToolKit.command and it worked. This did not work when I ran BCBToolKit.command file that was downloaded prior to the java install. Looks like a fresh copy of the folder needs to be unzipped for this to work.
I hope this helps future mac users out!
All the best,
FG
Hey Chris,
now I have a question about tractotron. The probability.xls file gives me values > 1. I am assuming that this should not be the case (expected values between 0-1?!)
Can you think of a reason why this happens?
Unfortunately it is a little complicated because I am using BCBToolKit on WSL Ubuntu…
Best regards,
J
I have CT and MR images of stroke patients, which I am normalizing in the Clinical Toolbox. Could you tell me the steps you took to “co-register” in SPM?
Hi Travis, apologies for the delay it was a long, well-deserved weekend :).
Maybe you can use the following code (provided that BCB toolkit is in your Application folder)
Open the terminal and try the following:
for a in *.nii.gz
do echo $a
echo "I love BCBtoolkit"
/Applications/BCBToolKitOSX/Tools/binaries/bin/flirt -interp nearestneighbour -in $a -ref /Applications/BCBToolKitOSX/Tools/extraFiles/MNI152.nii.gz -out r00$a.nii -usesqform -applyxfm
/Applications/BCBToolKitOSX/Tools/binaries/bin/fslmaths r00$a -mul r00$a -bin r00$a
done
It will resample your lesions and save it with the same name but with r00 in the front. Let us know if that works. mich.
Dear Chris,
i have yet another question about the bcb toolbox. Is there a way to do group comparisons using a discrete variable (i.e., whether a symptom is present or not; two groups, one symptom +, one symptom -; unfortunately for our question there is no continuous measure) with AnaCom2?
Best regards,
Julian
