Hello, Chris and Michel will be happy to answer all your questions about BCBtoolkit here! [shapeimage_2]

Ha sorry got you! This because when you non linearly aligned your lesion in the MNI space some voxels falls in between and therefore are tagged with a value between 0 and 1 according to the proportion of involvement of that voxels in the MNI space. You can threshold and binarise your lesion map at …

Hi Mich, Thanks for the clarification! That makes perfect sense now. I’ll go ahead and threshold the lesion map at 0.5 as you suggested. I really appreciate your help with this! Best regards, David

Hello. I’m having trouble with the output of “Disconnectome maps”. I have drawn Lesion on a T1 image converted with the command “Normalization” on the MNI152 template and put the mask image of Lesion in the command “Disconnectome maps”. I get an “End!” notification and the message “Data properly …

Hi Shun, It is weird indeed. Is your output folder different from the input folder?

Dear, Chris Thank you for replying. Whether the input and output folders are the same or different, an empty folder named “log” is created. Is it correct to map lesion to T1 registered in the MNI template output in “Normalized” command and put in “Disconnectome maps”? Do I need to do any additio…

Dear BCBToolKit Maintainers, I am having trouble with disconnectome maps. Therefore, I used the fslmaths function of FSL to analyze the NIfTI data of the MNI template showing the disrupted white matter fibers output by the tractotron. I would like to know if the results of the FSL analysis are val…

Hey, sorry for the delay. Just back from holiday. I’m sorry but we added this atlas upon request from our reviewers and are not in charge of its maintenance. All I could find is this page JHU DTI-based white-matter atlases . Good luck

Hi Shun, I’m sorry I am a bit confused with your request. I can run the analysis locally if you have any trouble. Feel free to reach out michel.thiebaut@gmail.com I would rather avoid flipping data in general.

@sawai.neuroreha did you use the Normalize module with the folder of T1 images as input and then used the “Apply transformation to other” option with the folder of the lesion masks as input? If so, this is a way to do it so it should have worked. Have you verified the normalized brains and masks a…

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BCBToolkit Questions

cchien November 6, 2024, 11:25am 161

JHU Tract NIFTIs missing, error using for Tractotron

Dear BCBToolkit Maintainers, When running Tractotron using the JHU Atlas within the BCBToolkit v4.1.0 (OSX) directory for tracts, there is an error given in the output xls files under SAF_MFG_IFG_L: Label does not exist, closest match is “SAF_SFG_IFG_L.nii.gz - Small associative fibres superior frontal - inferior frontal l gyri left” → although this NIFTI file for SAF_MFG_IFG_L does seem to exist in the directory. Also, with closer inspection the following tracts are only available in the d…

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