BCBToolkit Questions

63

Thanks for the positive feedback!

Yes it is possible if you change the code of the app.

I’m currently in holiday but if you can’t act me again in august I can modify the code for you.
Kind regards

Mich

64

Hi John,

If you want to do it yourself, I think you would just need to change line 41 in BCBToolkit/Tools/scripts/disco.sh:
tmp_tracto_mask=$tmp/tmp_tracto_${subj_name}
For:
tmp_tracto_mask=$tmp/tmp_tracto_${trk_name}_${subj_name}
The files will be in BCBToolkit/Tools/tmp/tmp_disco
trk_name is created just before, I think I was using it for that purpose but wanted to save some space.
Just be careful because when you rerun the disconnectome it automatically erases the temporary folder. So, be sure to save it somewhere else before you run another disconnectome :wink:

Hope this helps,
Chris.

It should just a

66

Hello Chris and Michel

I have an issue I did not understand with BCBToolKit.
here is the error :

"[I removed the path file in the message]/BCBToolKit/Tools/scripts/anacom_proper.sh: ligne 349: ${#co_perf}-1 : expression de sous-chaîne négative
Error in file(file, “rt”) : impossible d’ouvrir la connexion
Calls: create_list → read_txt_in_list → read.csv → read.table → file
Exécution arrêtée

I never faced this problem. I tried many times, by looking for the csv file, simplifying everything to prevent a problem in the csv (removing every dot, underscore, etc…). In the terminal the Cluster are performed up to the last patient 'Disco Clu : 0" but only for cluster 0, I have got 6 clusterx.nii, the maskedMeanValMap and the maskedStd so it is not a problem with the nifti file from my lesion directory…

I tried to understand the anacom_proper.sh file but I did not understand :frowning: and find the problem, I think it my be a “R” issue but I did not find what is different from other times when it worked.

Thank you for you help

Bests

Fabien

67

Hi Fabien,

Sorry you’re having issues with the BCBtoolkit.
It looks like R cannot access the csv file. But, it could come from something before that. Could you send me the log file by email so I can have a look?

68

Hi!

I’m trying to implement Disconnectome but I am getting an error:
/home/kgeier/scratch/BCBToolKitLINUX/BCBToolKit/Tools/binaries/bin/fslmaths: /lib64/libstdc++.so.6:
version `GLIBCXX_3.4.21’ not found (required by /home/kgeier/scratch/BCBToolKitLINUX/BCBToolKit/Tools/binaries/bin/fslmaths

So it seems to me that this is an issue with my Linux version not being sufficiently up to date to handle BCBToolkit. My Linux RHEL is 7.9 and I’m using gcc/9.3.0. I’m using a shared computing cluster that I don’t have the privileges to update Linux version for, so I am posting here to see if there are any ideas of how to work around this?

Thanks for any tips at all!
All the best,
Kirk

69

Graham_Error_BCBToolkit.txt (24.4 KB)

Btw here is the full error log if that is helpful!

70

Hi @KirkG ,

Have you tried installing updated GCC binaries in your own Anaconda environment? You can append the environment’s lib path to your LD_LIBRARY_PATH, so FSL can find it.

Best,
Steven

1 Like
71

So I’ve determined the problem is based on the computing cluster I’ve been using (Compute Canada/Alliance Canada) isn’t generally set up to have binary applications connect with the OS.

But they have a script to set the paths (instructions here: Installing software in your home directory - CC Doc). You run “setpaths --path YOURPATH_toBCBToolkit”

Not sure if any other users will be on Compute Canada but there it is!

72

Thanks again Steven!

73

Hi Chris and Michel and other gurus

I’m back with another question!

Essentially, I would like to know how we go from the disconnectome map which shows the white matter tracks connected to a lesion, to knowing which cortical regions are actually being (dis)connected to via this white matter (and are now no longer receiving certain input from the stroke).

I would look for any of my cortical ROIs that overlap with the disconnectome map, but the disconnectome map appears as a tract, and if thresholded for example to 0.5 does not come into physical contact or overlap with the grey matter.

I notice in figure 2 of the Foulon 2018 paper (Advanced lesion symptom mapping analyses and implementation as BCBtoolkit - PMC) that the cortical region being “disconnected” as it relates to the behavioural measurement but I can’t quite figure out from the methods how that works (or if it’s just looking at the actual lesions in that case).

This may be an issue of me having zero DTI experience so I apologize if this is a basic question.

74

Hi Kirk, the images from Foulon et al are the display of the significant results intersecting with the inner surface of the cortex (ie outer surface of the white matter).
The labelling is not made using regions but manually (we’re anatomists!). If you would like to do the same you can consult the anatomical pages of our book (Atlas of human brain connections 2012) or the recent one from Petrides (2019). Alternatively, if you still would like to use an automatic methods I would recommend not tresholding (our tractography in the background is clean). Cheers

75

Thanks Steven! Very helpful!

76

Dear Chris and Michel,
Thank you very much for developing the Toolkit and for having this forum for questions! And I’m trying to download BCBToolkit from http://toolkit.bcblab.com/ , but the website seems to be broken. It says that " NoSuchKey The specified key does not exist.No such object: bcblabweb/index.html/BCB/Softwares.html".
Looking forward to your reply.
Best regards,
Yaya Jiang

77

Hi Yaya,

Apologies, we are currently changing the website. You can still download BCBtoolkit from www.bcblab.com

Kind regards

michel

78

OK，Thank you very much!

79

Hi Michel:
I am trying to download BCBToolkit from new website (Page 1), but the download was always interrupted during ongoing process. It says that ‘unable to download, a problem has occurred’. I don’t know what caused it.
Thank you for you help
Bests
Ke Wu

80

Hi Chris and Michel,
I am trying to use the BCBToolKit(v4.1.0 BCBToolKitOXS) to create disconnectome maps.It is based on 10 healthy participants’ fibers (/BCBToolKitOSX/Tools/extraFiles/tracks/*.trk) by default. But many researches（Salvalaggio et al.,2020;Alves et al.,2021;Ulrichsen et al.,2021;Joutsa et al.,2022 and so on） created disconnectome maps based on HCP 7T data using BCBToolKit. I would like to know if BCBToolKit shares the .trk files of HCP 7T.
Thank you in advance,
Yaya

81

Hi Yaya,

Thanks for your interest in our work!

We are currently updating the website and the open data section is not available yet. Apologies.

Nevertheless you can download the trk here OSF | Disconnectome7T (as part of the material made available with Thiebaut de Schotten et al. Natcomm 2020). This is for MNI at 2mm let me know if you rather would like the version at 1mm.

Cheers
Mich

82

Hi Ke,

This should not be the case but as bcbtoolokit is quite big (7go) any interruption on your connection can stop the download :confused:
If you have a pro Dropbox account I can eventually share the folder with you?

Cheers

Mich

83

Hi Mich,

Thanks for the quick reply. Yes, it would be great to have the version at 1mm. :smiley:

Best wishes,

Yaya