NITRC MRIcron Forum: open-discussion

MRICRON overlap and descriptive statistics

VERA GRAMIGNA — Wed, 22 Jan 2025 11:24:00 GMT

Dear support,
I would like to solve some problems that I am encountering in my research. More specifically: -When I overlap flair.nii and lesion.nii (obtained from automatic software) in MRICRON, all appear correct. If I convert lesion.nii in voi, it is flipped. Is there a way to maintain the same reference system after conversion? -When I overlap overlapping map (alllesion.nii) on aal maps, using descriptive statistics, I obtain several parameters (numVox numVoxNotZero fracNotZero peak min mean meanNotZero).Can I have more information about the meaning of each of them?Is there a cutoff within which I must consider the damaged regions? Thanks

Nudge drawings in superior and inferior directions with hotkeys

Cassia Manting — Wed, 15 Jan 2025 7:57:43 GMT

Hi! I would like to nudge my drawing of a voxel in the Inferior and Superior direction using keyboard hotkeys as it is very difficult to do it by going to Draw-Nudge-Inferior and clicking on the mouse 30 times. I noticed that there are hotkeys for all the other 4 directions (i.e. Ctrl+Shift+L, Ctrl+Shift+R, Ctrl+Shift+P, Ctrl+Shift+A) but not for Inferior and Superior. Is there a way to configure this or can you add this function?
Thank you!

Citation

Chris Rorden — Sat, 11 Jan 2025 14:36:56 GMT

At long last, I have written a manuscript that describes MRIcron. If you use MRIcron for your publications, please consider citing
 
Rorden C (2025) From MRIcro to MRIcron: The evolution of neuroimaging visualization tools. Neuropsychologia, 207:109067. PMID: 39761848
 
https://pubmed.ncbi.nlm.nih.gov/39761848/

RE: "Integer required: Multi-volume file, please select volume to view. [1..2]" and "undo" steps

Chris Rorden — Sun, 17 Nov 2024 12:42:17 GMT

If you are just starting out, you may want to try the more modern MRIcroGL.. While I am glad that my MRIcron software has provien robust and popular, modern tools can better use contemporary hardware.
 
WIth regards to MRIcron:
<ol>
<li>If you load a 4D time series, MRIcron will ask you to select which 3D volume you wish to view. A single DICOM series can contain many 3D volumes (e.g. fMRI data is a 4D time series, and DTI is a collection of 3D volumes sensitized to different directions). You can either select the time series when you open a dataset, or use fslsplit to convert a single 4D NIfTI file to a series of 3D NIfTI files. With either option, I would start by using the MRIcron Import/ConvertDicomToNifti menu item to convert all of your DICOMs to NIfTI images. This will reduce the number of files (as it seems your data is in classic DICOM) and given them meaningful file names.</li>
<li>I agree, the drawing undo only has a single step, so you will want to be careful with each iteration. If you are using a MacOS or iOS device, you can try out our "NiiVue" application where the drawing mode allows multiple undos. We hope to release NiiVue for other operating systems soon.</li>
</ol>

"Integer required: Multi-volume file, please select volume to view. [1..2]" and "undo" steps

Hua Song — Sun, 17 Nov 2024 8:04:00 GMT

Dear All,

I hope this message finds you well.

I am a first-time user of MRIcron and am currently exploring its functionalities for ROI drawing. Despite reviewing the forum discussions, I still have some uncertainties regarding the import issue with NifTI and “undo” option, and I would greatly appreciate your insights on the following queries:

Q1: When importing a NIfTI file, I encountered the message: "Integer required: Multi-volume file, please select volume to view. [1..2]". However, my dataset only contains a single DICOM folder with multiple DCM files. Could you please clarify what selecting [1] or [2] means in this context? How does this choice impact my workflow?

Q2: While drawing the ROI, I chose the "autoclose pen" option, but mistakes are inevitable at times. I noticed that I can only undo one step, which makes it challenging when multiple errors occur, as I have to restart the drawing process entirely. Is there a way to increase the number of undo steps to improve error tolerance?

I greatly appreciate your guidance on these matters, and I look forward to your advice.

Warm regards,

Hua Song

Fudan University, Shanghai, China

RE: MRICron .nii size file not supported

Chris Rorden — Tue, 07 May 2024 16:28:48 GMT

You may want to try MRIcroGL (you can optimize the "Maximum Texture Size" for your graphics card in the preferences). You did not say what operating system you are using, but in general MRIcron on Linux and MacOS should handle 2gb (decompressed) images. If your image is compressed (.nii.gz) you may want to decompress it, as the original GZip format had a maximum size of 2Gb uncompressed and not all implementations support larger sizes.

MRICron .nii size file not supported

daniela bolanos — Tue, 07 May 2024 15:04:27 GMT

Dear all,
I want to open a .nii file from QSM with 420 MB, but when I drag the files to MRICron window, it doesn't appear anything. Is it possible to open in MRICron view? or why is the reason I can not see the .nii images?
Thank you so much!
Best regards,
Daniela Bolanos

RE: How to proceed with manual rotation as we have always done (old MRIcron fans)

Sara Bertagnoli — Mon, 08 Apr 2024 11:10:10 GMT

Dear Chris,
thank you very much for your message. Indeed, we tried to follow your instruction but we fail in our aim. The problem is that till now, in order to overlap various patients' lesions, we drew each single lesion in the axial slices of the normalized template given by the software. In other words we rotated (in the three dimensions, yaw, pitch and roll) the template, drew the lesion, and then re-rotated the patient's voi in order to put them in the MNI standard space and overlap among patients. As you said, this procedure is no more possible in mricron. We moved to MRIcroGL and we have watched the tutorials, but we cannot find some responses.  Can you help us?
These our questions:
<ul>
<li>is there the possibility to rotate the standard MNI152 template or should we rotate the patient's image after importing them in the system? How?</li>
<li>In case of drawing directly on the patient's image, how can we normalize its image in order to compare with other patients and atlas? Can you share instructions?</li>
<li>Once we have rotated and normalised, is the procedure for drawing and saving vois the same as in mricron?</li>
</ul>
Looking forward to hearing from you at the best of your convenience, we thank you again
sara (and gratefull team)

RE: How to proceed with manual rotation as we have always done (old MRIcron fans)

Chris Rorden — Sun, 25 Feb 2024 21:57:27 GMT

Can I suggest you try MRIcroGL. The Import/Tools/Rotation menu item shoudl guide you. While I am glad that MRIcron remains popular and mature, active development stopped over a decade ago (to MRIcroGL and eventually to NiiVue). The code is open source, so feel free to extend it if you wish to see new features.

How to proceed with manual rotation as we have always done (old MRIcron fans)

Sara Bertagnoli — Sun, 25 Feb 2024 15:23:00 GMT

Hi! So glad to have worked with NITRC tools since 2011, expecially with MRIcron. I found my OLd version 6 6 2013 that let us to rotate images following the tools : draw --> advanced --> rotate (and a little box with yaw, pitch and roll functions appears). 
I noticed that with the new versions created by this platform the rotation tool has been removed. I read in the forum a more or less similar request and in that case a concearning of Chris Rorden is that "Interpolating and reslicing data is a lossy operation". Does removing the ability to rotate have anything to do with this? 
In our studies we have always proceeded with double-blind procedures for the alignment of the templates and manual drawing rather than with automatic procedures (What we did was rotate the template to align with the patient scans, draw the VOIs, and then rirotate them). Would it be wrong to continue using the 2013 version to design a new study? How do you suggest we proceed if we aim to rotate manually? (sorry if maybe you put the rotation tool in other places instead 'Draw --> advanced' and I didn't see it, creating a long question for nothing :) )
Thank you in advance, 
Bw, Sara