With MRIcron
 Draw/MaskImageWithVOI
With MRIcroGL
 Draw/Advanced/MaskImage

The File/SaveAsNIfTI option saves the MRI scan you are viewing. This allows you to convert various image formats (MGH, NRRD, ECAT) to NIfTI. The Draw/SaveVOI option saves your drawing. This is described in the manual:
  https://people.cas.sc.edu/rorden/mricron/stats.html
If you are just getting started, and are using a computer built in the last decade, I would suggest you use the modern MRIcroGL instead of the legacy MRIcron
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage#Drawing_Regions_of_Interest
While I am glad that my classic tools have remained popular and robust, I have a heavy teaching, administration, service and research load, so have little time to support these older tools.

When you download a recent version of MRIcron (e.g. v1.0.20190902)
  https://www.nitrc.org/frs/?group_id=152
you will notice that it includes an executable dcm2niix in its 'resources' folder. The MRIcron "Import" menu item provides a graphical wrapper for dcm2niix, but you can also run it from the command prompt.

dcm2niix is the modern version of dcm2nii that includes support for BIDS output and enhanced DICOM.
  https://github.com/rordenlab/dcm2niix

dcm2niix does not know the intention of your sequences. A T2* scan might be a task fMRI in one series and a resting state acquisition in another. 

You may want to look at one of the many tools that wraps dcm2niix with your study-specific heuristics. Examples include ezBIDS, Heidiconv, and Dcm2Bids
  https://github.com/rordenlab/dcm2niix#li...

For future acquisitions, you can set the series name on your console to match your intention, e.g. "T1", "T2", "FLAIR". You can even do this to help automate conversion to BIDS data:
 https://github.com/ReproNim/reproin

Interpolating and reslicing data is a lossy operation. You will really want to use a dedicate tool like FSL's mcflirt or SPM's motion correction algorithm to deal with these effects. If you use AFNI, you can uses its motion censoring functions to detect and eliminate noisy artifacts.

Your data is anisoptropic. You can check the "Reorient images when loading" checkbox in preferences to interpolate the images, though note there will no longer we a one-to-one correspondence between screen pixels and image voxels. For future sequences, you may want to consider using isotropic sequences. 

You may also want to try MRIcroGL - I am glad that MRIcron has proved robust and popular, but I no longer have time to actively develop MRIcron.

Sounds like a question for the SPM forum:
  https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A1=ind2201&L=SPM&X=6A30DF6DC73478E1E1&Y=rorden%40sc.edu

You may also want to watch some of Andy's outstanding YouTube videos.

Hello,
 What version are you using? If you are using the pre-release (v1.2.20200707) https://github.com/rordenlab/MRIcroGL12/releases/tag/v1.2.20200707 you can change this by going to the Preferences window and setting the "Reduces volumes larger than ..." If you are using an older version of v1.2, you can select Preferences and press the "Advanced" button to edit the text file, in this case the value you want to edit is "MaxVox=560". The default setting is 560 which will work for all modern graphics cards. If you have a discrete graphics card with 8Gb of RAM, you can set this to 1024. This will stop the downsampling of large data.

Unfortunately, while changing this will hide the warning, in your case it will not make the resulting image look much better. In your example, the image has a exceptionally high in-plane resolution, but very thick slices. These thick slices make the image look blurry in the slice (head-foot) direction. This is an inherent property of your anisotropic image, any tool must interpolate this low resolution dimension. In future, you may want to consider acquiring isotropic images. For Siemens the classic 3D T1 sequence is referred to as "MP-RAGE" and the 3D T2 sequence is "SPACE" - both can provide outstanding isotropic images.

Hello,
why does the registration of MRI T1 image and fMRI fail when I use SPM12? After the registration, I use mricron to open the T1 image and the fMRI image at the same time (there is a yoke function in the view), they are not at the same coordinate origin, and sometimes even when viewing one image, the other image does not Appears in mricron's display area.
It will prompt: No overlap between overlay and background - these images do not appear coregistered.
Thank you very much for your help, looking forward to your reply~

These scans are anisotropic (slice resolution is higher in plane than between slices). Choosing the "Reorient images when loading" preference will reslice this data to be isotropic. Since you are just starting out, you may want to try MRIcroGL which leverages modern hardware. While I am happy that MRIcron is popular and has proved robust, it was designed for computer hardware from 2005.

Hello,

I suspect this is related to:
  https://github.com/nipy/nibabel/issues/1046
if you create these images with Python, please choose an appropriate precision for your data (e.g. dtype=np.uint8 for binary data)


Assuming your data is binary lesion maps (where each voxel is either lesioned [1], or unlesioned [0]), the 64-bit precision is not required, and you can dramatically reduce image size by storing them as UINT8, e.g.
  fslmaths ~/T1 -add 0 ~/T1c -odt char
or to save as 32-bit float:
 fslmaths ~/T1 -add 0 ~/T1f -odt float


 I am glad that my legacy popular remains popular. I have moved my own development on to NiiStat.
  https://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage
 Feel free to maintain and exend the NPM source code and project.

This is beyond the scope of my viewing software.
 1. Convert 2D PNG to NIfTI 2D
      https://stackoverflow.com/questions/52535729/convert-png-files-to-nii-nifti-files
 2. Convert 2D NIfTI to 3D NIfTI using Matlab, Python or fslmerge.
 3. Set the origin, orientation and scale. Perhaps SPM's Display function can help here. Be aware that CT scans of the brain were often acquired with gantry tilt, and the slices will be pitched relative to MNI space.

This question is underspecified. Are you trying to reorder the 2D slices in a 3D volume, or the 3D volumes in a 4D time series? Why ais the image order scrambled - what is the source of these images and how were they converted (e.g. did you convert them from DICOM to NIfTI using dcm2niix)? I suspect a combination of fslroi and fslmerge can solve your issue, but it might be easier to fix it at the source.

Hello,
 I am not very familiar with CentOS, but Wiki says that CentOS 7 was released in 2014, with full updates ending in 2020. I wonder if it does not the modern widget sets. Do some of the older releases work? 

https://www.nitrc.org/frs/?group_id=152

You could also try the pre-release for the upcoming version
  https://github.com/neurolabusc/MRIcron/releases
as noted in the release notes, the latest version expects libqt5pas, which you may be able to install from a rpm:
 https://github.com/davidbannon/libqt5pas/releases/tag/v1.2.9

Are these modern CT scans or is this an archival study? 

Once upon a time, CT scans were acquired with irregularly spaced slices (more near the brain stem, fewer slices for the cortex) and with substantial gantry tilt. The wide spacing between slices typically render these slices a poor choice for normalization. You may want to see if you can take a popular slice and angulate the volume to match the Damasio slides. My legacy MRIcro software has a "free rotate" button that helps, but you could also do this with SPM:
  https://people.cas.sc.edu/rorden/mricro/mricro.html


For modern CT scans, these images typically have good spatial accuracy in all planes and can be warped to standard space using my clinical toolbox for SPM. I would suggest using a modern MNI-oriented atlas rather than the legacy Damasio atlas, as this will aid translation to studies using other modalities.

I use Debian rather than RedHat Linux distributions. My best guess is that you can install the .rpm file from here:
  https://github.com/davidbannon/libqt5pas/releases
Given your hardware, I would suggest trying out MRIcroGL instead of MRIcon:
  https://github.com/rordenlab/MRIcroGL/re...
MRIcroGL uses OpenGL 2.1, which was released in 2006. As long as your computer supports OPenGL 2.1, I strongly suggest using MRIcroGL instead of MRIcron. MRIcroGL will leverage the dedicated hardware and 2048 cores of your graphics card.

I provide MRIcroGL for both GTK2 and QT5. Again, QT5 will require the libqt5pas library.

I am happy that my old software is mature and remains popular. However, MRIcron has not been updated in the last decade. You may want to try out MRIcroGL that leverages recent advances in computers:
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage
I suspect with your overlay, you simply have to set the minimum and maximum values for the layer for the desired contrast. The algorithm that guesses the default contrast when loading an image does not know your intention, and may not always be ideal. I would suggest the notes on the Layers in the manual
  https://people.cas.sc.edu/rorden/mricron/main.html

Choose the Display/Multi-Planar menu item to see the axial, coronal and sagittal images simultaneously. You can click on the image to navigate to different coordinates, or use the controls in the "2D Slice Selection" panel.

You can also choose Display/Mosaic to create custom multi-slice views. You can use the widgets in the "Mosaic" panel to crudely set these values, or input custom text for fine control The Scripting/Templates/Mosaic and Scripting/Templates/Mosaic2 menu items show how you can control these views with a Python script. 
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage#Mosaic_Views

For the MacOS, all applications are folders. From the Finder, you can right-click (or Control-click if you are using a trackpad) on the program icon and select "Show Package Contents". Be aware that Apple has started to require notarized applications, and depending on your version of MacOS, modified applications make not work after you changed them, as Apple fears that the program has been tampered with. This is an issue with recent versions of MacOS, and is not specific to my software.

NPM has been replaced by NiiStat.

You may want to look at the Power and PowerMap scripts
  https://github.com/neurolabusc/NiiStat

NPM has been replaced with NiiStat:

https://www.nitrc.org/plugins/mwiki/inde...
https://github.com/neurolabusc/NiiStat

Alternatively, you may want to look at PALM:
  https://github.com/andersonwinkler/PALM

Modern SPM works well with single file NIfTI (filename.nii), so I am not sure why you need the dual file version (.hdr/.img). I have moved active development to MRIcroGL, so the MRIcron documentation might be getting a bit out of date.

I would use the FSL tool fslchfiletype to do this, but you could also use a Matlab script with SPM:



function nii_nii2hdr (fnms)
%Convert file.nii to file.hdr/file.img
% https://github.com/rordenlab/dcm2niix/is...
%n.b. FSL does not like file.nii and file.hdr co-existing
% fnms : (optional) images to convert
%Examples
% nii_nii2hdr
% nii_nii2hdr('T1_LM1003.nii');
% nii_nii2hdr(strvcat('T1_LM1003.nii','T2_LM1003.nii'));

if ~exist('fnms','var') %file not specified
[A,Apth] = uigetfile({'*.nii';'*.*'},'Select .nii file(s)', 'MultiSelect', 'on');
fnms = strcat(Apth,char(A));
end
for i=1:size(fnms,1)
fnm = fnms(i,:);
[pth, nm] = spm_fileparts(fnm);
hdr = spm_vol(fnm);
img = spm_read_vols(hdr);
hdr.fname = fullfile(pth, [nm, '.img']);
spm_write_vol(hdr,img);
end

Development of that tool ended 6 years ago. Even at that time, it recommended that you upgrade to dcm2niix. The DICOM standard has evolved a lot since that time, with vendors now supporting enhanced DICOM. I strongly suggest you use dcm2niix:
  https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
If you prefer a graphical interface, get MRIcroGL (Import/ConvertDICOMtoNIfTI menu item):
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage

While I hope my legacy software is mature and robust, I am a full time scientist and instructor. I can not support old tools. It is an open source project, so you can always maintain and extend it as you wish.
  https://github.com/neurolabusc/MRIcron

Will you just tell me please what does the following message mean while converting dcm2niigui?

"Warning: for compatibility, converting UINT16->FLOAT32, range: 63064
If you prefer file size over compatibility, edit your preference named UINT 16 to FLOAT32"