Hello,

this is so trivial that I apologize in advance!

I have installed the latest version of MRIcroGL on my Mac Pro but don't seem to be able to load 4D NIFTI images. I wonder if this is a known issue and if there is a workaround? Nothing happens after I load the *.nii.gz containing 600 images but I can load individual NIFTI images with no issues.

I'm guessing this is related to this specific environment, since MRIcroGL works alright in other Macs I have access to. This is happening on a Mac Pro Intel running Mac OS Sonoma 14.4.

Here is the information displayed by About:

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1.2.2022070b Cocoa x86-64 LLVM

Author: Chris Rorden

License: BSD 2-Clause

Version 14.4 (Build 23E214) MacPro7,1

Retina Scale: 2

ATI Technologies Inc.; OpenGL = 2.1

ATI-5.5.17; Shader=1.20

2.1 Max 3D texture: 16384

Current texture: 207x246x215 43mb

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Any help will be greatly appreciated! Thank you very much.

Best wishes,

E.

I have reorientated (and resliced) some brain scans in SPM12 which display correctly in SPM but "lose" their reorientation when loaded in MRIcroGL.

MRIcron has an option in preferences to "reorient images when loading" and the images then load in the correct orientation. Is there any equivalent that would allow me to do the same in MRIcroGL?

Dear all, 

I have used MRICroGL to create some nice brain images, which I am going to publish as part of my article.

The journal is requesting me to include in the manuscript some form of permission / acknowledgement for use of the MRICroGL outputs, which is fair and I will obviously mention the use of MRICroGL.

However, I am not sure exactly how to do this. I wonder if you could let me know how to acknowledge the use of this software? Is there any sort of boilerplate language that covers it? Also, is there any licensing / accreditation required linked to the MRICroGL? 

Thank you in advance for your help!

Best wishes,

Paula

Hi there,

Is there a version of dcm2niix that handles the new dicom compression from the SIEMENS 3T scanner software version syngo_MR_XA30?

I've been having trouble converting dicoms to nifti using dcm2niix ever since we upgraded.  The scanning sequences now seemed compressed with what I think is a JPEG2000 format. Before the software upgrade, when we pushed a scan to USB, it would create a directory stucture based on scan number and type, and produce one dicom for every slice.  Now, after the upgrade, all the dicoms get dumped to the root directory of the USB or DVD, and many dicoms are compressed into one. It's now hard to identify the sequences without converting them for the dicom headers or json files, and kind of a pain even after converting them.

When I try to use dcm2niix to convert them, I get a long stream of error messages like the following:

Chris Rorden's dcm2niiX version v1.0.20230411  (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)
Found 1171 DICOM file(s)
Warning: Compressed image stored as 64 fragments: if conversion fails decompress with gdcmconv, Osirix, dcmdjpeg or dcmjp2k export_enhanced_dicomdir/24013123/53410001/67783417
Image Decompression is new: please validate conversions

I have tried to decompress the files using all four recommended tools, and I have tried using dcm2niix for Windows and Linux, verions V1.0.20230411 and V1.0.2171215.

One of the decompression utilities finally worked - but the process was quite a pain.

Is anyone else seeing this?  I'm hoping there's a better way that I just missed.

Thanks so much for the help,

Sherri

Hello, 

I have a macbook 2021 (M1 pro, Ventura 13.4.1) that wont allow running the latest MRIcroGL version.  the error says access violation, clik ok to ignore or abort. both do nothing.

As reading a similar error in the forum, I have granted permissions to open internet software, moved the file to the app folder, used chrome to download, and run from the terminal (with the image attached showing error 'cannot find AFNI atlas path').

so not sure where the issue is and any help is very appreciated!

thanks

Hi, all, 

I am new to MRIcroGL. I am wondering if MRIcroGL can set Yoke as default when I open images. Then how can I change the window size? The default one is too large for me. Will it work if I change the script? 

Thanks, 

Cornelia

From looking at the gl library, there seems to be no way of accessing the volume data for mathematical operations. For example aplying a mask, or doing some sort of bias field correction from python. Because of that I was wondering what would be the way of incorporating new libraries. I've replaced the python35.zip and python35.dll and with an "updated" version, in my case a python3.7 but when I try to import numpy I get an error. Initially numpy was not found, but after appending site-packages to sys.path  (sys.path.append(sys.path[0]+'\\site-packages') ) it is found, but still not able to load.

import sys
sys.path.append(sys.path[0]+'\\site-packages')
print(sys.path)
import numpy

output

Running Python script
['C:\\Users\\Claudiu\\bin\\MRIcroGL\\Resources\\python37.zip', 'C:\\Users\\Claudiu\\bin\\MRIcroGL\\Resources\\python37.zip\\DLLs', 'C:\\Users\\Claudiu\\bin\\MRIcroGL\\Resources\\python37.zip\\lib', 'C:\\Users\\Claudiu\\bin\\MRIcroGL', 'C:\\Users\\Claudiu\\AppData\\Roaming\\Python\\Python37\\site-packages', 'C:\\Users\\Claudiu\\bin\\MRIcroGL\\Resources\\python37.zip\\site-packages']
Traceback (most recent call last):  File "C:\Users\Claudiu\bin\MRIcroGL\Resources\python37.zip\site-packages\numpy\core\__init__.py", line 22, in <module>  File "C:\Users\Claudiu\bin\MRIcroGL\Resources\python37.zip\site-packages\numpy\core\multiarray.py", line 12, in <module>  File "C:\Users\Claudiu\bin\MRIcroGL\Resources\python37.zip\site-packages\numpy\core\overrides.py", line 7, in <module>ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:Traceback (most recent call last):  File "<string>", line 6, in <module>  File "C:\Users\Claudiu\bin\MRIcroGL\Resources\python37.zip\site-packages\numpy\__init__.py", line 150, in <module>  File "C:\Users\Claudiu\bin\MRIcroGL\Resources\python37.zip\site-packages\numpy\core\__init__.py", line 48, in <module>ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troublesh...

Please note and check the following:

  * The Python version is: Python3.7 from "C:\Users\Claudiu\bin\MRIcroGL\MRIcroGL.exe"
  * The NumPy version is: "1.21.6"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'
Python Successfully Executed

Just wanted to briefly report some unusual behavior:

I have only recently been experiencing some odd behavior, where whenever I wanted to close MRIcriGL (running on Windows 10) I get an error popping up telling me ".MRIcroGL12.ini cannot be created as it is being used by another program" with the options "OK" (keeping the window open) and "Abort" (which then closes the application). This persisted even when freshly installing MRIcroGL. 

(I had previosly mentioned running MRIcroGL in compatibility mode as a potential workaround but actually this did not resolve the problem).

Any suggestions are highly appreciated. 

Thanks for creating and continuously improving MRIcroGL! 

BR

hello! I would really appreciate some help. When running Advanced -> Interpolation between slices -> All sagittal gaps the program runs as if "All axial gaps" was selected instead. So, when interpolating, a message saying "no gaps found in the axial direction" shows up instead. How can I fix it?

HI, I was trying to run Python script with MRIcroGL, but every time I click run, or cmd+r, the whole application would dispear. I tried using sample script and reinstall MRIcroGL, but it still cannot run scriprt. BTW, I was running it on MacOS Sonoma with a M1 chip.

Hello,

I notice when generating cluster table outputs, the voxel coordinates are in the underlay space. Is it possible for them to be in the overlay space? E.g., if I have an overlay in 1x1x1mm resolution but use the default MNI152 brain in ~.7x.7x.7mm resolution I get standard coordinates in sub mm increments. It would be a bit more convenient if the resolution of these coordinates were based on the overlay maps. My current work around is to simply use an underlay that is the functional or lesion map, and then generate the cluster tables, but it would be easier if one did not need to do this. 

Thanks!

Jeremy

Hello,

I am trying to use MRIcroGL via a notebook to generate a volume with edges from a cluster image. However, the save function, gl.saveimg(), seems to be limited to saving the bg image. Is there any way you can specify an overlay for saving to an .nii image?

Could you please provide citation information, so I can correctly cite it in an article? Thanks

Thanks to another thread, I was able to find the python command for changing overlay Depth

  gl.shaderadjust('overlayDepth', x)

where x is overlayDepth.

As far as I can see, the default for overlayDepth is 0.1, but I'm not sure what the units are. thanks

It would be really helpful also to have this covered in the python commands on Github. It mentions shaderadjust, but it's not easy to see what commands are covered, and an example of the various things that can be adjusted would be very helpful.

To show stimulation sites in our experiment, I want to do the following steps through coding:

1) Draw spheres  (e.g., Sphere1 center: 20 5 10, radius 2 mm; Sphere2 center: 25 51 11, radius 2 mm) .

2) Show these ROIs with different colors (I need five colors for five ROIs ) on rendered brain.

3)  Cutout the rendered brain to improve visualisation. For example, I need to cutout the brain to show the sphere centered around  20, 5, 10. I need to know how to transform the coordinates into the inputs which could be used by the cutout function gl.cutout.

Do you know how to do this through codeing in MRIcroGL?

I checked the manual and demo scripts and didn't find corresponding code except for the cutout function.  But this function doesn't accept coordinates as its inputs.

Hello, I have a set of simple python scripts that do everything I need by applying overlay to MRI images and saving the resulting images. I would like to execute MRIcroGL WITHOUT the GUI. I know that I can start the execution from the command line but it looks like MRIcroGL always start the GUI even if the script does not require it. It looks like there is no option from the command line to turn off the GUI. Any possible trick?

Thanks in advance and best regards,

Mario

I have SPM T map which is obtained with SPM12 group statistical analysis. the features of this T maps include: p  value=0.05, exthended thresholding  T=4.83(based on table in SPM12), minimume of cluster size>10 voxel. Now I want to find regions with significant differences by using of AAL parcellation atlas. my questions:

1-How can I change the option in MRIcroGL based on these values which i find in SPM12?

2- I get these result in MRIcroGL, but I can't underestand these numbers in paranthesis.

Notes: rspmT_0002(interpolated) on aal(interpolated)
Volume    Peak    PeakXYZ                 Peak Structure    • XYZ    Structure
434            7.7     -21.2×-31.9×-37.1                                    -27.1×-34.8×-39.3    Cerebelum_10_L(51) -(19)                                                                                                    Cerebelum_7b_L(16) Cerebelum_8_L(7)                                                                                                               Cerebelum_6_L(6)