Summary:
I would like to obtain the MNI coordinates of the center of a cluster of particularly intensely bright voxels. I see that I can get the X,Y,Z coordinates of a cluster of particularly intensely bright voxels but would like to know how to get the MNI coordinates of that cluster. How can I do that?
More information:
I am working on a dataset of ~100 participants with lesions. I segmented and normalized my T1 images to MNI space, registered my native FLAIR images to my standardized T1 images so now the FLAIR images are also standardized, ran these images through the Lesion Segmentation Tool (LST) Lesion Growth Algorithm (LGA) pipeline (Schmidt et al., 2012), and obtained two output images: a version of the FLAIR and a lesion probability map. The lesion probability map is a binary map (each voxel is either white with an intensity of 1 indicating that voxel is a lesion or dark with an intensity of 0 indicating that voxel is not a lesion). Both files are .nii.
I open both of these images (the FLAIR as an image and the lesion probability map as an added overlay) into MRIcroGL. I then select the lesion probability map, click "options", "generate cluster table with options", and then set the threshold intensity to be 1 and the minimum cluster size to be 0. I obtain a table that tells me the volume and X,Y,Z coordinates of each lesion.
How do I get the MNI coordinates of each lesion?
(also, what exactly are the X,Y,Z coordinates? what space is that in?)
Note:
I read some posts that told me I can enter MNI coordinates and then view that brain location. I don't want to enter MNI coordinates, I want to be given MNI coordinates.
Any assistance you might be able to provide would be greatly appreciated. Additionally, please let me know if my question and/or explanation did not make sense.
Thank you so very much,
Emily Harriott
PhD student, Vanderbilt University
Hello Emily!
I just ran into the same problem. Did you find a solution?
Thank you in advance!
Anna
Dear Anna,
Unfortunately, no good solution for you. :/ I'm so sorry! Broadly, what I'm planning to do instead is put everything in MNI space, then transform the T1 to the FLAIR, and then using python and with a different file for each gray matter reegion, count the voxels of lesion in each region (this gets me really what I wanted in the end). I haven't done this yet, though, so crossing my fingers it works.
If you can get the image(s) into MNI space, I think you can use xjview within spm12 within matlab to see the coordinates of the center of the cluster? - if you load the T1 and the lesion map (or perhaps just even the lesion map?) and then click 'select cluster' or 'pick cluster/info' and then look at the command window (you should get the peak coordinates and center of mass coordinates for each cluster in addition to the list of regions that cluster is in/touches)?
Please let me know if you find something!
Thank you,
Emily
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No update. This is outside the remit of MRIcroGL. The project is open source, so feel free to add this feature (and submit a pull request if you wish to share it with the community). MRIcroGL is mature and stable, and will likely see only point releases going forward. You may want to take a look at NiiVue which we are actively working on with the AFNI, FSL, FreeSurfer and nilearn teams. NiiVue can be embedded into web pages, standalone applications, jupyter notebooks, vscode, etc. Since it is written in JavaScript, it is inherently scriptable.