neurolabusc / mricrogl10_old Goto Github PK

When you are viewing an image in multi-plane mode, and happen to click in an empty area in the left tool bar (even by accident), the display mode will automatically switch to "render". I discovered by accident. Not sure if intentional, but it was disorienting because I clicked on a button-less area and things happened.

Hello,

Nuñez et al (2018) https://doi.org/10.1371/journal.pone.0199239) introduced an optimized colormap that is more inclusive of people with color vision deficiency. Maybe this optimized version of viridis, named cividis could be incorporated into MRIcroGL and SurfIce?

I have added a clut file for cividis; I looked up the colors used in viridis and replaced them with the corresponding RGB from cividis. A naive version of clut with all 256 nodes (which is not practical) is also attached. I have changed the extension from .clut to .txt
cividis.txt
cividis255.txt

A quick side-by-side comparison of viridis (left) and cividis (right) is below:

Resources:
Details on clut format: https://www.nitrc.org/forum/message.php?msg_id=26007
Examples of cividis: https://www.ncl.ucar.edu/Document/Graphics/ColorTables/cividis.shtml
https://github.com/marcosci/cividis

Hello, again I'm having issues building MRIcroGL:

>>> Emerging (2 of 2) sci-visualization/mricrogl-1.0.20160930::neurogentoo
 * mricrogl-1.0.20160930.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                                     [ ok ]
>>> Unpacking source...
>>> Unpacking mricrogl-1.0.20160930.tar.gz to /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work
>>> Source unpacked in /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work
>>> Preparing source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930 ...
SetupCompilerFilename: Searching compiler ...
SearchCompilerCandidates Value=fpc File=/usr/bin/fpc
Hint: (lazarus) [RunTool] /usr/bin/fpc "-iWTOTP"
Hint: (lazarus) [RunTool] /usr/bin/fpc "-va" "compilertest.pas"
SetupCompilerFilename: using /usr/bin/fpc
Hint: (lazarus) storing Lazarus directory "/usr/share/lazarus/" Compiler path "/usr/bin/fpc" in "/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/homedir/.lazarus/environmentoptions.xml"
TProject.DoLoadStateFile Statefile not found: /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/lib/x86_64-linux/simplelaz.compiled
Info: (lazarus) Execute Title="Compile Project, Mode: Release, Target: MRIcroGL"
Info: (lazarus) Working Directory="/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/"
Info: (lazarus) Executable="/usr/bin/fpc"
Info: (lazarus) Param[0]="-B"
Info: (lazarus) Param[1]="-MDelphi"
Info: (lazarus) Param[2]="-Scgi"
Info: (lazarus) Param[3]="-CX"
Info: (lazarus) Param[4]="-Cg"
Info: (lazarus) Param[5]="-O3"
Info: (lazarus) Param[6]="-Xs"
Info: (lazarus) Param[7]="-XX"
Info: (lazarus) Param[8]="-vewnhibq"
Info: (lazarus) Param[9]="-Fi/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/lib/x86_64-linux"
Info: (lazarus) Param[10]="-Fl/opt/gnome/lib"
Info: (lazarus) Param[11]="-Fu/usr/share/lazarus/components/PascalScript/Source/lib/x86_64-linux"
Info: (lazarus) Param[12]="-Fu/usr/share/lazarus/components/opengl/lib/x86_64-linux/gtk2"
Info: (lazarus) Param[13]="-Fu/usr/share/lazarus/lcl/units/x86_64-linux/gtk2"
Info: (lazarus) Param[14]="-Fu/usr/share/lazarus/lcl/units/x86_64-linux"
Info: (lazarus) Param[15]="-Fu/usr/share/lazarus/components/lazutils/lib/x86_64-linux"
Info: (lazarus) Param[16]="-Fu/usr/share/lazarus/packager/units/x86_64-linux"
Info: (lazarus) Param[17]="-Fu/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/"
Info: (lazarus) Param[18]="-FU/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/lib/x86_64-linux/"
Info: (lazarus) Param[19]="-oMRIcroGL"
Info: (lazarus) Param[20]="-dLCL"
Info: (lazarus) Param[21]="-dLCLgtk2"
Info: (lazarus) Param[22]="simplelaz.lpr"
Hint: (11030) Start of reading config file /etc/fpc.cfg
Hint: (11031) End of reading config file /etc/fpc.cfg
Free Pascal Compiler version 3.0.0 [2016/05/04] for x86_64
Copyright (c) 1993-2015 by Florian Klaempfl and others
(1002) Target OS: Linux for x86-64
(3104) Compiling simplelaz.lpr
(3104) Compiling uscaledpi.pas
(10001) PPU Loading /usr/share/lazarus/components/opengl/lib/x86_64-linux/gtk2/openglcontext.ppu
(10011) PPU Source: openglcontext.pas not found
(10028) Recompiling OpenGLContext, checksum changed for LCLProc
/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/openglcontext.pas(12,46) Fatal: (10022) Can't find unit OpenGLContext used by LazOpenGLContext
Fatal: (1018) Compilation aborted
Error: /usr/bin/ppcx64 returned an error exitcode
Error: (lazarus) Compile Project, Mode: Release, Target: MRIcroGL: stopped with exit code 256
ERROR: failed compiling of project /var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930/simplelaz.lpi
 * ERROR: sci-visualization/mricrogl-1.0.20160930::neurogentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line 115:  Called src_compile
 *   environment, line 2313:  Called die
 * The specific snippet of code:
 *       lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi || die
 * 
 * If you need support, post the output of `emerge --info '=sci-visualization/mricrogl-1.0.20160930::neurogentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-visualization/mricrogl-1.0.20160930::neurogentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930'
 * S: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20160930/work/MRIcroGL-1.0.20160930'

It seems openglcontext is missing. But it is not missing:

zenbookhost ~ # grep "openglcontext" /var/db/pkg/dev-lang/lazarus-1.6.0-r1/CONTENTS
obj /usr/share/lazarus/components/opengl/lazopenglcontext.lpk f2fef0ec026f3bed484bedb01308e6a9 1439757725
obj /usr/share/lazarus/components/opengl/example/testopenglcontext1.lpr ae1eb0aa2c5f2b600363ef3a23ac268d 1175864361
obj /usr/share/lazarus/components/opengl/example/testopenglcontext1.lpi fca66882bbc535702918e176a010b8b3 1448004584
obj /usr/share/lazarus/components/opengl/lazopenglcontext.pas eef257134591055be44ecabd78df1a54 1439757725
obj /usr/share/lazarus/components/opengl/openglcontext.res e970a6433b1c82b2e47c68944786f214 1380946572
obj /usr/share/lazarus/components/opengl/openglcontext.pas dc5da7e1910f57428a76a14e8c69f5c8 1443363088
obj /usr/share/lazarus/packager/globallinks/lazopenglcontext-0.0.1.lpl e781c3be8e28d3b8b569a64223013795 1291294415

Any idea what's going on here?
For reference, I am using lazarus-1.6.0-r1 and fpc-3.0.0.

Continuation from rordenlab/dcm2niix#242

I suggest to change the default output format to at least include %d and to extend the tooltip or the default message in the console to include all formatting options. Indeed, only %d allows to disambiguate some sequences (eg, MoCoSeries on Siemens machines, and pretty much any dual stream sequence).

Here is a comparison:

%t_%p_%s: 20140519131916_ep2d_bold_repos_7.nii
%f_%p_%t_%s: DICOM_ep2d_bold_repos_20140519131916_7.nii
%n_%t_%p_%d_%z_%s: NAME_20140519131916_ep2d_bold_repos_MoCoSeries__epfid2d1_64_7.nii

I suggest these changes as the GUI is presumably made for people who do not like or are not accustomed to using the commandline, and formatting options are currently mostly accessible only via commandline, which prevent adequate use from most GUI users.

Hi, I would be interested in using MRIcroGL to create figures as part of my data analysis scripts.

It does not seem like the program has an API. Do you think it would be worthwhile or feasible to create one?

lso, does MRIcroGL use conversion to VTK as an itermediary step to rendering?

Hi,
When I use MRIcroGL to convert a coronal scan into a nifti image, I have a problem. I try two ways to do this by using MRIcroGL. The first is to save nifti images directly by "File-> Save NIFTI". The second is to save nifti images by the following command “dcm2niix.exe -f 'output_filename' -i y -l y -p y -x I y -v y -z y -o 'output_path' 'input_path' “. Both of the above-generated results are different. The image shape using the first way is (X, Y, Z): 320 x 85 x 320, which is my desire. However, the image shape using the second way is (X, Y, Z): 320 x 320 x 85. Because I will deal with a lot of coronal Dicom files, I want to use the second way for batch processing. But it will happen the above error. How to do this using the command?

Best wishes,
Jianhong Cheng

I have a few supersampled NIfTI's I would like to visualize with MRIcroGL, they seem to work down to a resoution of 0.018x0.018x0.018mm, they display as a homogenous bIue (?) volume at 0.017x0.017x0.017mm, and fail to open downwards from 0.016x0.016x0.016mm, giving the following error:

Image dimensions do not make sense (x*y*z*bpp = 840*1275*643*4)

Here are the images, the original image from which they were supersampled, and the code with which I did so. I am unsure whether this is an MRIcroGL issue, or whether the files is simply corrupted, but I don't see why the dimensionality should not make sense.

in mosaic view, the slice text shows up inside the brain. the user can turn it off, but when it's on, being inside the brain isn't ideal. I attempted to find where in the code this happens, but came up empty handed.

I showed slides from MRIcroGL to my colleagues recently. When a colleague spotted edge effects, I was getting nervous about our analysis. It turned out, the data were fine, but OVERLAYLOADSMOOTH introduces edge effects (the phenomenon is highlighted in the manual).
My request: Please get rid of the edge effects.
Proposed solution:
I don't know how smoothing is achieved in MRIcroGL, but I think this effect could be avoided by

1. creating a binary in parallel to the overlay
2. smoothing the overlay
3. printing the smoothed overlay, dividied by the smoothed binary mask instead of the smoothened overlay.
   (at least that's how its done with Gaussian smoothing in SPM)
   Keep up the good work! Cheers, Matthias

Feature request: could we enable multiple undo's (ctrl-z) for roi drawing?

Dear Chris,

I am transitioning from MRIcron to MRIcroGL for my everyday NIfTI viewing needs, as MRIcron does not support anisotropic images very well (it downscales in every dimensions, including the ones of higher resolution).

I would just like to request if it would be possible to detect the first positional argument as an image to open. Indeed, I am trying to use MRIcroGL as my default app to open nii files, and when I do so it does not open the file, so I guess it's because I have to supply a switch to tell it this is an input image, but it's usually a more involved process to provide a custom commandline in most windows managers (in particular Windows 10 that I am using).

I installed Lazarus, downloaded the latest source and tried running the code on windows 8.1. I got an error:
Error reading ScriptForm.DesignTimePPI: Unknown property: "DesignTimePPI"
Any idea what's going on here?

My idea was to increase left-hand panel width in mricrogl (should not be too difficult). Currently the panel is too narrow and makes using overlays very difficult (see figure). In some earlier version there was separate pop-up window for overlays. That was much better.

While testing your software on multiple linux machines (I am working on packaing it for Gentoo Linux) I noticed two issues with it. These issues persist both with my Gentoo Linux build of your sources, and with your precompiled binaries:

• The MRIcronGL interface does not work with gtk3 - ldd tells me it uses gtk2 libgtk-x11-2.0.so.0 => /usr/lib64/libgtk-x11-2.0.so.0 (0x00007f13bb3e2000), is there any way to build it for gtk3?
• Overlays do not work. I tired importing one or more overlays, and I get an additional colorbar for each, but no actual picture is being displayed. I have checked that the overlay and base image are in the same coordinate space, and tried to play arounf with most of the sliders.

Please see the following screnshots for examples (the second image should have the third image overlaid on it):

Thank you for the additional colorbar-options in the last update of MRIcroGL.
I've noticed a bug when setting the Font/Colorbar size in Preferences > Advanced.
After editing MRIcroGL.ini (e.g. by changing ColorbarSize=0.03500000015 to
ColorbarSize=0.01500000015) the colorbar is resized for all display options, with the exception of MOSAIC, which ignores the ColorbarSize (regardless of whether the GUI or the script is used).
Generally, a function to flexibly change ColorbarSize or Font sizes in Scripting would be awesome.
Cheers, Matthias

Somehow, whenever I use the save as bitmap function, images come out with blue tint, especially for overlay images. Attached are the screenshot of the console, and the image generated with save as bitmap.

I'm using the precompiled MRIcroGL 1.2.20190902++ GTK2. Load up any image and overlay, and overlay color will come out with blue tint when saved as bitmap.

Screenshot:

Saved file:

Hi, I get the following error in a window pop up when I try to visualize volumes in “render” mode:

Shader compile error 0:1(10): error: GLSL 3.30 is not supported. Supported versions are: 1.10, 1.20, 1.30, 1.00 ES, 3.00 ES, 3.10 ES, and 3.20i ES

Additionally, the rendering looks like a block in rainbow colors.

This happens on:

• =mricrogl-1.0.20170401
• =mricrogl-1.0.20170714
• =mricrogl-1.0.20180623
• =mricrogl-9999 (latest commit, 2fad294)

This does however, only happen on one of my machines. Any idea what could be wrong?

Hi all,

I am using MRIcroGL in order to create some brain visualizations.

I have an activation map and I need to use a cyclic colormap such as the HSV colormap. however, such option is not available.

Any tip?

I also posted this here: https://www.nitrc.org/forum/forum.php?thread_id=11413&forum_id=4442

Hi,

I created a zstatistic image and was looking at it in mricrogl and it looks weirdly broken. I wanted to ask, if you could maybe tell me why is that the case? I attached image and screenshot in the following link:
https://www.dropbox.com/sh/84ybhf2ltx8y9nt/AABi-XyttR-xkDxRABTgBScHa?dl=0
Thanks and best

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?

MRIcroGL can make really outstanding visualizations of the brain with a quite simple to use GUI, congratulations for the great work!

However, I can't find a way to save PNG/JPG images with a higher resolution than the window size on my screen (I looked in the GUI and in scripting). Would it be possible to add a "enlargement" option when saving, so that we can save the image at 2x/3x/5x resolution of window size?

@neurolabusc you recently mentioned the package could be built without Python scripting support.

Sadly I am having trouble building the python4lazarus module (upstream does not support lazbuild, and the Lazarus forums could not help out thus far either).

In case I have to drop python4lazarus, how can I build mricrogly in its absence?

I am currently getting this error:

silenthost ~ # emerge -av mricrogl

 * IMPORTANT: 5 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.


These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  N     ] sci-visualization/mricrogl-1.0.20181111::chymeric  0 KiB

Total: 1 package (1 new), Size of downloads: 0 KiB

Would you like to merge these packages? [Yes/No] y

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) sci-visualization/mricrogl-1.0.20181111::chymeric
 * mricrogl-1.0.20181111.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                 [ ok ]
>>> Unpacking source...
>>> Unpacking mricrogl-1.0.20181111.tar.gz to /var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work
>>> Source unpacked in /var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work
>>> Preparing source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111 ...
cp: cannot stat '/etc/lazarus': No such file or directory
SetPrimaryConfigPath NewValue="system-lazarus-config" -> "/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111/system-lazarus-config"
SetupCompilerFilename: Searching compiler ...
SearchCompilerCandidates Value=fpc File=/usr/bin/fpc
Hint: (lazarus) [RunTool] "/usr/bin/fpc" "-iWTOTP"
Hint: (lazarus) [RunTool] "/usr/bin/fpc" "-va" "compilertest.pas"
SetupCompilerFilename: using /usr/bin/fpc
Hint: (lazarus) storing Lazarus directory "/usr/share/lazarus/" Compiler path "/usr/bin/fpc" in "/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111/system-lazarus-config/environmentoptions.xml"
Error: (lazbuild) Broken dependency: python4lazarus_package
 * ERROR: sci-visualization/mricrogl-1.0.20181111::chymeric failed (compile phase):
 *   (no error message)
 *
 * Call stack:
 *     ebuild.sh, line 125:  Called src_compile
 *   environment, line 785:  Called die
 * The specific snippet of code:
 *       lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" simplelaz.lpi || die
 *
 * If you need support, post the output of `emerge --info '=sci-visualization/mricrogl-1.0.20181111::chymeric'`,
 * the complete build log and the output of `emerge -pqv '=sci-visualization/mricrogl-1.0.20181111::chymeric'`.
 * The complete build log is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111'
 * S: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111'

>>> Failed to emerge sci-visualization/mricrogl-1.0.20181111, Log file:

>>>  '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/temp/build.log'

 * Messages for package sci-visualization/mricrogl-1.0.20181111:

 * ERROR: sci-visualization/mricrogl-1.0.20181111::chymeric failed (compile phase):
 *   (no error message)
 *
 * Call stack:
 *     ebuild.sh, line 125:  Called src_compile
 *   environment, line 785:  Called die
 * The specific snippet of code:
 *       lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" simplelaz.lpi || die
 *
 * If you need support, post the output of `emerge --info '=sci-visualization/mricrogl-1.0.20181111::chymeric'`,
 * the complete build log and the output of `emerge -pqv '=sci-visualization/mricrogl-1.0.20181111::chymeric'`.
 * The complete build log is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111'
 * S: '/var/tmp/portage/sci-visualization/mricrogl-1.0.20181111/work/MRIcroGL-1.0.20181111'

The current software always shows images using neurological convention (left anatomy on left of display). Request feature to optionally display in radiological convention, left anatomy on right of display. Mirror Coronal and axial slices, but not rendering. Ensure drawings are loaded/saved correctly.

Contingent on the famous mandelbug not occurring, I can compile but not execute MRIcroGL (e92f6da). I get a popup stating:

Error reading ScriptForm.DesignTimePPI:
Unknown property: "DesignTimePPI".
Press OK to ignore and risk data corruption.
Press Cancel to kill the program.

From the command line, I get:

[FORMS.PP] ExceptionOccurred 
  Sender=EReadError
  Exception=Error reading ScriptForm.DesignTimePPI: Unknown property: "DesignTimePPI"
  Stack trace:
  $00000000004A28D6
  $00000000004A1B99
  $00000000004A35C5
  $00000000004D3F7B
  $00000000004D31A1
  $000000000044B6BD
  $000000000044DE2C
  $0000000000455831
TApplication.HandleException Error reading ScriptForm.DesignTimePPI: Unknown property: "DesignTimePPI"
  Stack trace:
  $00000000004A28D6
  $00000000004A1B99
  $00000000004A35C5
  $00000000004D3F7B
  $00000000004D31A1
  $000000000044B6BD
  $000000000044DE2C
  $0000000000455831

Hey there :-)

It would be great to have the ability to choose more colors for overlays, for example by having a color picker for the starting and ending color (or simply a uniform color, that would work as well!). Indeed, particularly when additive is enabled, it can become a bit complicated to display more than 5 overlays at once (as some additive colors will display as another color, eg blue and red will become purple but purple might be assigned to another overlay).

PS: this feature would also be amazing in Surf Ice as well ;)

Hey folks, is there any timeline on when the pre-compiled version will be updated on NITRC? I did attempt a compile myself, but ran into a number of difficulties. Thanks for the excellent software, couldn't science nearly as well without it.

Hey there,

Not a bug but a question: how does MRIcroGL recognizes atlas in nifti files from normal nifti files?

Indeed, there is no option to force the activation of atlas coloring (coloring each region depending on its integer value), so I guess this is automatically detected from the nifti, but how? What does the nifti file needs to include to be detected as an atlas?

Thank you very much in advance!

Recently I tried to rebuild my live mricrogl version, and I got this crash log. As you might notice, this is very resemblant of a recent issue with mricron.

So I tried what you suggested there:

• lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi works nicely in the cloned repo.
• lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi --ws=carbon fails.
• lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi --ws=cocoa fails.
• lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi --ws=gtk2 fails.
• lazbuild -B --lazarusdir="/usr/share/lazarus/" simplelaz.lpi --ws=gtk3 fails.

I would like to package your software for Homebrew, it would be very nice I you followed http://semver.org guidelines when tagging/releasing over here in GitHub :)

When drawing, I make a few ROI masks, and was not able to use ctrl+z to undo, but clicking undo in the draw menu worked.

If you go to view -> extract brain, and cancel the popup window by clicking the x icon, then the app proceeds to continue and ask you for an image to brain extract (even though the user cancelled).

Hello,

these need to be replaced in order to compile on Ubuntu 20.04, I have replaced them with PyLong_fromLong and PyUnicode_fromString, compiled, but I do not know if it will have any consequences later. I don't know how to configure Lazarus to use Python 2.

Feature request: enable left-dragging on numbers in colorbar to adjust contrast and overlay thresholds?

For precision's sake, I like to browse images in MRIcroGL by using the keyboard bindings for navigation (left/right, up/down, home/end).

Sadly, however, this navigation does not update the position as reported in the window title bar, so whenever I reach a desired position I have to click the mouse exactly on the crosshairs to get the coordinated. this usually throws the positiion off a bit, and sometimes that actually is critical.

Would you be interested in adding such an enhancement?

If you go to view -> extract objects, and then close the popup window with the "x" button (like you changed your mind and don't actually want to use the feature) it still acts as though some processing is going on in the background (spinning beach ball in MacOS).

I am trying to get the new scripting features installed, but running:

lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="with-packages" simplelaz.lpi

This seems to successfully compile and results in this log, but will not produce any "*.py*" files I can place into my $PYTHONPATH. See the output of tree after running the aforementioned command, here.

Perhaps expectedly, python -c 'import gl', gives me:

ModuleNotFoundError: No module named 'gl'

Am I misunderstanding how this is supposed to work, or has lazbuild omitted to build something?