4D Overlays

[TheChymera]

If I have multiple volumes in a NIfTI file (e.g. a merged NIfTI from multiple subjects) - is there any way to flip between these volumes in the GUI?

[neurolabusc]

No, MRIcroGL loads one 3D volume at a time. When you select a multi-volume dataset you are requested to select which volume to load. If you use Macintosh OSX, you can use the "MRIcro" application that comes with MRIcroGL - it loads complete 4D datasets, you scroll through images using the scroll-wheel of your mouse, the vertical swipe of your trackpad or the View/Next;View/Previous menu command: https://github.com/neurolabusc/MRIcro Another option would be FSLview. Feel free to modify the code to support this, though given modern multi band sequences (where a single fMRI run can create more than 32Gb of data) you may want to add a preference that only loads the initial volumes (MRIcro allows you to either load some or all 4D volumes). Loading all the volumes of a huge dataset will lead to slow loading and fewer resources for other programs. It is also possible to exhaust your RAM if you build a 32-bit executable.

-c

[TheChymera]

So MRIcro only works on OSX? For some reason I do not get prompted to select the volume in mrocrogl.

Any ideas what could be wrong?

[neurolabusc]

Here is a sample 4D dataset - you should be prompted to select a volume when you File/Open the image. If not tell me the version of MRIcroGL and Operating system you are using: https://www.dropbox.com/s/90esio4xbo4hqyx/Fieldmaps006.nii.zip?dl=0 Yes, while MRIcroGL is cross platform, MRIcro is built using Xcode and therefore is OSX only. MRIcro exploits a lot of functions specific to OSX, so while it is mostly written in C it would be a real challenge to port to any other operating system (except maybe iOS).

[surchs]

Can confirm that the supplied example data does not open a prompt to select the volume along 4th dimension.

MRIcroGL 64-bit Linux  (GTK2)  7 February 2017
 www.mricro.com :: BSD 2-Clause License (opensource.org/licenses/BSD-2-Clause)
 Dimensions 207x256x215
 Bytes per voxel 1
 Spacing 0.74x0.74x0.74
 Description  spm - algebra
 OpenGL 3.0 Mesa 12.0.6 GLSL 1.30
Press "Abort" to quit and open settings /home/surchs/.MRIcroGL/MRIcroGL.ini

[neurolabusc]

I can not replicate your problem. I downloaded MRIcroGL 64-bit Linux (GTK2) 7 February 2017 from the NITRC web site and ran it on my CentOS 6.6 machine. Every time I open Fieldmaps006.nii with MRIcroGL (either dragging and dropping or selecting it using the File menu) I am prompted to select whether I want to view the 1st or 2nd volume. The only time I am not prompted to select a volume is if I restart the software and it was the last open image - in that case it assume I want to view the first volume (which is the desired behavior for a quick launch).

Note it only loads a single volume at a time, you can not flip between volumes (unlike the MacOS MRIcro software). The design is to minimize RAM usage and maximize speed.

What Linux distribution are you using? Have you tried restarting from the command line with "./MRIcroGL -r" - this should reset the program to its default settings.

[surchs]

I start MRIcroGL from the command line and then add the Fieldmaps006.nii as an overlay through the GUI. I don't get prompted to select the volume in that case. Maybe there is a difference in how we do the same thing.

[surchs]

Yeah, I think I misunderstood what you mean by loading the file. When I 'drag and drop' as you describe, I get the prompt. Also when I open through the file menu. What I was looking for was a way to select the volume of the overlay.

[neurolabusc]

OK, the latest source code now prompts you when you for a volume number when you load a 4D overlay. Typically, overlay's are 3D datasets, so I am not sure this is a common issue. However, it does now give the user feedback that there are multiple volumes.

[surchs]

Excellent, thanks for that.