NITRC MRIcroGL Forum: help

RE: Convert dcm to nii

Chris Rorden — Thu, 27 Jun 2024 19:04:59 GMT

This is out of scope for MRIcroGL and dcm2niix. The NIfTI files created by dcm2niix reflect the series as acquired on the MRI scanner. ChatGPT can help you write a simple Python script to concatenate your NIfTI, bval and bvec files. However, be careful as head motion may have occurred between sereis, phase encoding polarity may have changed, shim may have changed, or other properties may vary across series.
Rob Smith's insightful comments seem relevant to this question
https://community.mrtrix.org/t/concatenate-and-average-dwi-data/4029/2

Convert dcm to nii

Dimitrios Samaras — Thu, 27 Jun 2024 18:41:36 GMT

Hello, I'm using MricroGL to convert dcm images to nii. I have 2 sets of DWI one of them for b=50 and one for b=800. I want the converted nii file to convert both images into a single nii file. Is it possible?

RE: MNI template version

bgu123 — Wed, 15 May 2024 20:31:24 GMT

Understood, thank you!

RE: MNI template version

Chris Rorden — Wed, 15 May 2024 15:48:23 GMT

Sorry, I would think visual inspection you applied would be the best method.

RE: MNI template version

bgu123 — Wed, 15 May 2024 6:53:25 GMT

Thank you for that information!  I downloaded 2009a, 2009b, and 2009c from the website then pulled up all 3 in MRIcroGL. However, they all look the same to each other and 'mni152.' Is this the best way to verify which version 'mni152' is, or do you suggest other steps I should take?

RE: MNI template version

Chris Rorden — Tue, 14 May 2024 12:10:58 GMT

Your screenshot shows the File menu from the Main menu. The main menu provides settings that influence ALL images. Note that MRIcroGL can load multiple images simultaneously that can each have different properties. Therefore, to find details regarding a specific image you must select it in the "Layers" panel and choose image specific options from the "Options" drop down menu in the Layers panel. Note that this drop down menu has an option named "Show header". The image is visibly Asymmetric. 
 
Since the header does not report if it is 2009a, 2009b or 2009c I would assume it is the original (2009a) version before the revisions were added, but you can test this assumption yourself:
https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
 
https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

RE: MNI template version

bgu123 — Mon, 13 May 2024 22:06:14 GMT

Sorry for my poor phrasing and sorry if I am misunderstanding your response.
Here is my re-phrased question: is the "mni152" template found within MRIcroGL (by going to File > Open Standard > mni152) the same as the ICBM 2009b nonlinear asymmetric MNI template?
I was also unable to find the options you described (see screenshot):

RE: MNI template version

Chris Rorden — Mon, 13 May 2024 10:38:02 GMT

By choosing "Show Header" from the "Options" pull down menu, you can see in the "Description" of the "Optional" tab that the sould of the image is:
www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
The image has been cropped and resliced to be 256 voxels in the longest direction.

MNI template version

bgu123 — Sun, 12 May 2024 21:24:24 GMT

Hi,
I was wondering if there are more details on the exact version of what the ICBM152 template is? For example, is it the ICBM 2009b nonlinear asymmetric MNI template?
Thank you

RE: Trouble loading 4D NIFTI images on Mac OS Intel (Sonoma 14.4)

Norberto Nawa — Mon, 01 Apr 2024 2:13:59 GMT

Dear Chris,
thank you for the advice. I've attempted to use the Metal version of MRIcroGL but unfortunately it does not seem to be able to load the 4D NIFTI either in my MacPro 2019.
I will use MRIcroGL in another machine while I wait for an update from Apple (though I am not holding my breath :-)
Cheers,
E.
 
Originally posted by Chris Rorden:
<blockquote>
I can not replicate this on any of my machines. It appears that the computer that is causing issues is a MacPro 7,1 from 2019 which were only offered with AMD Radeon graphics cards https://support.apple.com/en-us/102887
Macs with AMD graphics cards depend on Apple drivers, and these have not seen much support, especially as Apple has moved to manufacturing their graphics cards in house. I think it is telling that the graphics driver reports "ATI Technologies Inc.; OpenGL = 2.1", as AMD acquired ATI in 2006!
https://en.wikipedia.org/wiki/ATI_Technologies
Once upon a time, ATI cards only supported power of two textures, and your data is not a power of two: 207x246x215. 
You might want to see if the version of MRIcroGL that uses Metal directly instead of OpenGL (MRIcroMTLforMacOS_Sonoma) works:
https://github.com/rordenlab/MRIcroGL/releases
If this fails, I am afraid you are at the mercy of Apple's driver team, that has little incentive to support this old but capable hardware.
</blockquote>