NITRC MRIcroGL Forum: open-discussion

RE: Coordinates with False Precision

Chris Rorden — Tue, 21 Oct 2025 12:28:15 GMT

The title bar of MRIcroGL reports     X×Y×Z (i×j×k) = v Where XYZ is the crosshair location in world space, the ijk is the crosshair position in image space, and v is the voxel intensity at that location. The world space location is estimated using the orientation information of the NIfTI header (with precedence for the matrix-based sform). When an image is converted from DICOM to NIfTI, the world space origin is the isocenter (for MR scans) or table center (for CT scans). After normalization the world space origin should be the anterior commissure. The software does not make any assumptions about the precision of the data or the spatial transform. MRIcroGL assumes the spatial transform is truthful. It is simple a matrix transformation of the image space to world space. NIfTI assumes Talairach-Tournoux coordinates (RAS, such that XYZ are L->R, P->A, I->S). For more details:   https://brainder.org/2012/09/23/the-nifti-file-format/   https://en.wikipedia.org/wiki/Transformation_matrix#Examples_in_3_dimensions   https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html   https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Spatial_Coordinates

Coordinates with False Precision

Sebastian Brstilo — Mon, 20 Oct 2025 20:01:40 GMT

Hi everyone,
I am just curious about the coordinates that MRIcroGL is displaying in the top left of the screen. The coordinates that MRIcroGL give is to 4 decimal places, which seems like false precision to me and I am wondering how those values were calculated and if those are MNI coordinates or just coordinates related to the program software. 
Thank you in advance!

RE: Inquiry About Catani Natbrainlab Atlas for White Matter Tract Overlay in MRIcroGL

Hua Song — Thu, 20 Mar 2025 9:18:44 GMT

Dear Chris,
Thank you very much for your guidance! I was able to locate the Natbrainlab atlas and successfully extract individual tracts for mapping. Your help made the process much smoother.
I really appreciate your support!
Best regards, Hua Song

RE: Inquiry About Catani Natbrainlab Atlas for White Matter Tract Overlay in MRIcroGL

Chris Rorden — Wed, 19 Mar 2025 15:54:05 GMT

I would use the File/Atlas/natbrainlab menu item.

Inquiry About Catani Natbrainlab Atlas for White Matter Tract Overlay in MRIcroGL

Hua Song — Wed, 19 Mar 2025 8:23:19 GMT

Dear MRIcroGL Support Team,
I am currently using MRIcroGL and would like to overlay white matter tract contours onto slices to examine the spatial relationship between white matter tracts and lesions. Specifically, I am looking for a version of the Catani Natbrainlab Atlas that includes white matter tracts.
Could you please advise where I can download this atlas? I would greatly appreciate your guidance.
Thank you for your help.
Best regards, Hua Song

RE: Coloring Yeo &Buckner Atlas

Chris Rorden — Mon, 16 Dec 2024 14:40:37 GMT

Hello,
  You could certainly follow that approach. However, if you are just starting this now, it might be worth developing an atlas to work with NiiVue rather than MRIcroGL. As NiiVue has been adopted by many teams (AFNI, FSL, FreeSurfer, OpenNeuro), this can ease sharing. 
The relevant description of the NiiVue labels is here:
https://github.com/niivue/niivue/blob/main/docs/development-notes/colormaps.md#atlases-and-labeled-images
 
The live demo lets you apply your own colormap by inserting it into the text entry on the web page:
https://niivue.github.io/niivue/features/segment.html
A nice feature of NiiVue, is that it supports both voxels and labels, so your solution will work for both representations.

Coloring Yeo &Buckner Atlas

Beatriz Catoira — Mon, 16 Dec 2024 14:29:36 GMT

Dear Chris, 
I have already read the information that you had about ussing custom atlases but the atlas I am trying to add gives still some issues.
I have two atlases (Yeo 2011 for the cerebrum and Buckner 2011 for the cerebellum) loaded as Atlases to use in MRICroGL. What I would like to do it is to change the colors for each network assigned automatically to match the colors that they have in their original atlases:   1     Visual    120  18 134   2     Sensorimotor    70 130 180   3     DorsalAttention   0 118  14    4     VentralAttention 196  58 250    5     Limbic 220 248 164    6     Executive 230 148  34   7     Default 205  62  78 For this I have created a .lut file using python, with the same name as the atlas and filled in the first 7 rows (with the colors mentioned above) and padded the rest of the 256 rows with zeros. However when I try to load the atlas with the lut file it only shows some random regions in red. Am I missing something important I had to add to the lut file?
Thanks in advance!

RE: 4-d nifti overlay

Christopher Hyatt — Tue, 03 Sep 2024 20:53:24 GMT

Originally posted by Chris Rorden:
<blockquote>
The attached image shows a sample 4D image that you can replicate with File/OpenStandard/pcasl
1. The quick way to choose a volume is to click on the volume in the timeline. The timeline is the bottom panel - it is collapsible so make sure it is visible.
 
2. You can use a script using the `volume()` function. You can see all the functions with Scripting/Templates/help menu item. The script panel is on the right, so expand it if is collapsed. Like other tools, volume number is 0-indexed, so the 60th volume is 59. For me, the volume() does not refresh the image so I use the orthoview() function to force a refresh. So a script would look like this:
import gl gl.volume(0,3) gl.orthoviewmm(0,0,0)
</blockquote>
Chris, thank you!

RE: 4-d nifti overlay

Chris Rorden — Tue, 03 Sep 2024 20:35:13 GMT

The attached image shows a sample 4D image that you can replicate with File/OpenStandard/pcasl
1. The quick way to choose a volume is to click on the volume in the timeline. The timeline is the bottom panel - it is collapsible so make sure it is visible.
 
2. You can use a script using the `volume()` function. You can see all the functions with Scripting/Templates/help menu item. The script panel is on the right, so expand it if is collapsed. Like other tools, volume number is 0-indexed, so the 60th volume is 59. For me, the volume() does not refresh the image so I use the orthoview() function to force a refresh. So a script would look like this:
import gl gl.volume(0,3) gl.orthoviewmm(0,0,0)

4-d nifti overlay

Christopher Hyatt — Tue, 03 Sep 2024 19:42:35 GMT

I apologize if this question has been asked before, but is it possible, when loading 4-d Nifti overlays that contain a large number of 3-d functional or ICA maps, to jump to a particular volume within the 4-D nifti file? For example, I have 100 ICA component maps in a 4-D Nifti file and want to jump to volume #62 (of 100). Is there a way to do this without doing 'right click- Next volume' to go one by one to the volume I'm interested in?
Thanks,
Chris