NITRC MRIcroGL Forum: help

MRIcroGL color bar for negative darkest and brightest colors

Hannah Hafner — Wed, 21 Oct 2026 17:51:42 GMT

Hi,
We are using MRIcroGL to plot beta values across the brain, which means we are sometimes plotting a range of negative beta values. 
For the negative beta values, when I set the darkest value to a lower negative number (eg. -0.4), and the brightest value to a higher negative number (eg. -0.1), the color bar is oriented where -0.1 would be on the left and -0.4 would be on the right. If I switch the darkest and brightest, it still does not change the orientation of the color bar. Is there a way to flip the color bar when plotting a range of negative numbers so in this example it would go from -0.4 on the left to -0.1 on the right? 
Thank you,
Hannah

RE: Autoscaling of Darkest/Lightest values and find max voxel in overlay

Christopher Hyatt — Sat, 18 Apr 2026 22:29:06 GMT

Chris, I used Codex and added the option to turn Darkest/Lightest autoscaling off. Seems to work fine. See attached for Options menu item. So need to add this feature.  
Is there a python script that I could write to find the max (or min/most neg) voxel in an overlay?

RE: Autoscaling of Darkest/Lightest values and find max voxel in overlay

Christopher Hyatt — Sat, 18 Apr 2026 0:30:36 GMT

Chris, thanks for the help.
I'm not sure how to use niivue. It looks promising, but seems like one needs to know javascript to make it work. Is there a tutorial?

RE: Autoscaling of Darkest/Lightest values and find max voxel in overlay

Chris Rorden — Fri, 17 Apr 2026 11:24:22 GMT

I will see if I can extend MRIcroGL. Note that we already have this feature in NiiVue, as shown by the "per-volume contrast" check box in this live demo: https://niivue.com/demos/features/timeseries2.html

Autoscaling of Darkest/Lightest values and find max voxel in overlay

Christopher Hyatt — Fri, 17 Apr 2026 0:24:13 GMT

I often scroll through 4-D nifti overlays (ICA components, maps, etc) and I created a volume_select Python script to move quickly to a different overlay. However, every time I move to a new overlay volume, the Darkest and Brightest values do some sort of autoscaling.

A great option would be to turn off autoscaling and retain the values I set for the Darkest and Brightest values (e.g., for z-scored overlays, Darkest at 1.0 and Brightest at say 4.0 or 5.0). I created another Python script called minmax to set these values, but it doesn't appear that I can keep both volume_select and minmax open for running at the same time, but I don't want to have unload and load the two python scripts.

I have the Lazarus source code and the Lazarus compiler, and can compile/link source to binary successfully. I haven't coded in Pascal though since the 1980's, but I do know C/C++. Is there some source code I could change/add to the code to add a button box to turn autoscaling on/off?

Also, is there a way to python script finding the max (or min) voxel value in the current overlay? I see there are cluster options, but I'm not sure how to use this to find max or min peak voxel values in an overlay.

Thanks so much,

Chris

MRIcroGL: Problem with loading image

jcoryn — Fri, 05 Sep 2025 13:04:19 GMT

Hello, 
I experience problems with opening MRI images in MRIcroGL. I receive the error "File smaller than described in header (expected 20971872, found 16781312)", while I opened the exact same file yesterday without any problems. Could someone help me with this? 
Kind regards

MRIcroGL citation

Chris Rorden — Thu, 24 Jul 2025 13:22:59 GMT

For those who use MRIcroGL in for their work, I would be grateful if you would consider including this citation
Christopher Rorden (2025) MRIcroGL: voxel-based visualization for neuroimaging. Nature Methods. doi: 10.1038/s41592-025-02763-7 https://www.nature.com/articles/s41592-025-02763-7

Changing color scheme for atlas overlays

Maria Misiura — Mon, 20 Jan 2025 21:28:18 GMT

Hi, all! I am trying to create a figure with specific regions from the AAL atlas to visualize clusters of regions (i.e., precuneus, precentral, paracentral lobule all in one figure), but would like all of the clusters to be the same color. Is there a way to do this using the python scripts and the built in aal atlas? I have attached a screenshot of the figure and I would like all ROIs to be the same color

RE: Saving a file from generateclusters

Zdenek Linha — Fri, 17 Jan 2025 13:52:18 GMT

I am using Windows 10 and MRIcroGL 1.2.20211006

RE: Saving a file from generateclusters

Chris Rorden — Fri, 17 Jan 2025 13:47:35 GMT

Are you using MacOS, Linux or Windows?