NITRC MRIcroGL Forum: help

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?

RE: Setting the overlay search path the same folder as the open image

Doug N — Fri, 17 Jan 2025 13:38:55 GMT

Hi Chris, 
I'm using Windows 10 and MRIcroGL 1.2.2021106.
Doug

RE: Setting the overlay search path the same folder as the open image

Chris Rorden — Fri, 17 Jan 2025 13:16:04 GMT

What operating system are you using? MacOS, Linux or Windows?

Setting the overlay search path the same folder as the open image

Doug N — Fri, 17 Jan 2025 12:29:15 GMT

Hello, 
 
Just wondering if it is possible to adjust the settings in some way so that when you try to open an overlay it automatically opens the folder that the image layer is in? I believe this was the case with MRIcron and is very helpful for quickly searching for the appropriate overlays. Now it seems to open with the last folder you searched for in MRIcroGL. 
 
Thanks! 
 Doug

Saving a file from generateclusters

Zdenek Linha — Wed, 15 Jan 2025 9:54:38 GMT

Dear Chris,
is there a way to automatically save the table generated by function gl.generateclusters()? I know that you can save it manually but I have many patients and it would save me a lot of time to generate a .txt file for each patient with the contents of this table.
Thank you in advance,
Zdenek

RE: MRIcroGL - slice timing correction

Belina Rodrigues — Mon, 04 Nov 2024 22:07:38 GMT

Thank you.