Reply To: matrix connectivity estimation from my ROI


Hi Luca, It is possible to compute connectivity matrix from custom ROIs, with assumption that your custom ROIs are in the same space as .bfc.nii.gz file and is saved as a .nii/.nii.gz file. Also note that Brainsuite’s connectivity viewer only shows ROI IDs between 100-999. So, you may need to make sure that all your custom ROI ids lie in this range.

You would need to do few more things to ‘import’ your custom ROIs in BrainSuite. First, make sure that your label file with custom ROIs overlay correctly with bfc file in brainsuite. Then, you have to make a label description xml file, which would contain the information (like name etc) about each custom ROI. This xml file would be equivalent to brainsuite_labeldescription.xml file generated by running SVReg and should follow the same format. Below, I have shown an example of contents of xml file for two ROIs. The “id” field represents the voxel values in the custom label file. You can create this xml file in any text editor like notepad. Note that this xml file should contain description of all ROIs in your custom label file.

<?xml version="1.0" encoding="utf-8" ?>
<label id="196" tag="" color="0xff0000" fullname="My ROI 196"/>
<label id="122" tag="" color="0x0000ff" fullname="My ROI 122"/>

Now, you can load diffusion data along with bfc file by dragging and dropping the appropriate .bst file (generated by BDP) in Brainsuite. Then, open painter tool (Tools menu > Painter tool) to load custom ROI label and custom xml file. Load the custom label file by clicking the button with ‘open folder’ icon. Load the xml file you created by clicking on ‘Load Desc.’ button. At this point, you should be able to run tractography followed by connectivity computation in diffusion toolbox and your ROIs should showup on the circle plot.