Problem in how to extract roi

Hi mrtrix3 community

i have question about how to extract ROI
Because i want to analyze the different hemisphere of the brain separately, are there some methods to separate the right and left hemisphere of brain and track the nerve fiber in different hemisphere of brain, or extract the roi of specific position of brain?

thans for the respond

1 Like

Hello @1113 San,

You may have labels for your brain data. So, you may use mrcalc to extract ROI. Equals to the option may be fine. You may have a natural numbers like 1, 2, 3, of the labels, right? So, you can easily extract your region of interest (ROI).

I hope this will answer your question.

Best Regards,

Hello suren
Thanks for your reply
there is another question about analysis of fiber track.
if i just want to track the nerve fiber in left hemisphere or right hemisphere, how should i do?

i am sorry for this trouble

looking forward to your reply
γƒͺ エむγƒͺ

Hello γƒͺ エむγƒͺ,

そうですね、I think such type of label exists or maybe you can use some MATLAB or ITKSNAP tricks to create on your own.

How many labels do you have actually?

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Prior to analysis one typically creates a mask_image, a binary image that when layered over the MR image covers the entire brain to constrain computation only within that space and not outside (or in CSF). One could try to mrcalc the halfway point, but I highly recommend simply opening the brain and mask image in a viewing/editing software like FSL, going to edit mode, and erasing the left side and saving it as the right_hemi_mask and doing the same for the left side. Andrew Jahn has a video on custom mask creation on YouTube entitled β€˜Using FSLeyes, Part 4: Atlases and ROI Drawing’ from 2017.


Thanks for your respond

it helped me a lot

ruili Li

Hello! suren
i have a problem about how to create the connectome
According to the instruction, I had used the following command to process the label convert and create the connectome which is based on the template of FreeSurfer, but i do not know how to create the connectome based on template AAL90. in this case, how should i change the command to create the connectome based on template AAL90

labelconvert sub-CON02_recon/mri/aparc+aseg.mgz $FREESURFER_HOME/ FreeSurferColorLUT.txt /usr/local/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt sub- CON02_parcels.mif


γƒͺ エむγƒͺ

Hello Ruili,

Would you please post your issue or error from your terminal in detail? There may also be some issues while using the AAL90 template.