rschurade / braingl Goto Github PK
View Code? Open in Web Editor NEWAutomatically exported from code.google.com/p/braingl
License: MIT License
Automatically exported from code.google.com/p/braingl
License: MIT License
Option to lock (and unlock) dataset properties of the two views for when you
want the parameters to be the same and only the zoom and rotation to be
different between views.
Original issue reported on code.google.com by [email protected]
on 24 Jul 2013 at 8:48
it would be great if there was a possibility to delete colormaps. Right now it
seems to be necessary to remove the config-folder to get rid of ugly
colormaps...
Original issue reported on code.google.com by [email protected]
on 24 Oct 2013 at 3:42
1. Open BrainGL + nifti file --> Main window fits on screen
3. Open glyphset --> main window expands beyond bottom of screen
When the main window expands there is no way to make it smaller. Tabs in the
dataset properties windows also expand beyond the screen making it impossible
to switch between tabs without pulling the dataset properties window out of the
main window (which then obscures view of main gl window). When you then move
around the pulled out windows, they constantly try to jump back in to the main
window and screw up your previous arrangements, forcing you to spend 2 minutes
resizing all of the windows.
Original issue reported on code.google.com by [email protected]
on 4 Jul 2013 at 8:10
More screenshot options would be nice, i.e. to be able to select if you want a
screenshot of main gl 1, main gl 2, or the entire braingl window.
Original issue reported on code.google.com by [email protected]
on 20 Aug 2013 at 9:32
High priorities:
-color mapping of the surface
-visibility of stuff
-more general solution later
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:31
Placing the screenshot option in the "Help" menu might be not so intuitive. A
toolbar button would be helpful to enable single-click screenshots from
anywhere you are in the program.
Original issue reported on code.google.com by [email protected]
on 28 Oct 2013 at 9:09
It would be helpful to be able to choose whether the crosshairs are rendered in
one view, both views, or neither view (instead of simply on/off)
Original issue reported on code.google.com by [email protected]
on 13 Nov 2013 at 10:26
It would be helpful to provide a link to the web documentation in the "Help"
menu
Original issue reported on code.google.com by [email protected]
on 28 Oct 2013 at 10:02
What steps will reproduce the problem?
1. loading a functional dataset
2. creating an isosurface with the toolbar button
3. opening maingl2
What is the expected output? What do you see instead?
the isosurface is not shown in maingl 2
Please use labels and text to provide additional information.
Original issue reported on code.google.com by [email protected]
on 15 Nov 2013 at 12:28
What steps will reproduce the problem?
1. Unchecking "render crosshair" in general properties
2.
3.
What is the expected output? What do you see instead?
The crosshair disappears but the tick in front of the "render crosshair"
function in the "options" menu does not. It does work vice versa though.
Please use labels and text to provide additional information.
Original issue reported on code.google.com by [email protected]
on 28 Oct 2013 at 9:34
Setting the minimum threshold of a glyphset file to a negative value doesn't
work. The glyphs appear exactly the same as when the the minimum threshold is
set to 0.0.
Original issue reported on code.google.com by [email protected]
on 13 Nov 2013 at 3:23
What steps will reproduce the problem?
1. load textures
2. gauss filtering and delete old textures
3. memory load is increased
What is the expected output? What do you see instead?
constant memory
What version of the product are you using? On what operating system?
current - linux
Original issue reported on code.google.com by [email protected]
on 19 Nov 2013 at 9:44
Crashes when you click file>save, without having loaded any datasets (only
likely to happen by accident)
To reproduce:
1. Open brainGl
2. Choose file>save
Original issue reported on code.google.com by [email protected]
on 8 Jan 2014 at 1:23
-Using the color maps into the connectivity values
-constant color
-coordinates instead of direction
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:26
It would be useful to be able to paint in gradients to indicate uncertainty
and/or gradual/unabrupt transitions between neighboring areas, perhaps using a
slider to change the gradient of the selected paint color.
Original issue reported on code.google.com by [email protected]
on 15 Jul 2013 at 2:24
copied fibers need to retain their extra values
saving/loading needs to keep extra data intact
Original issue reported on code.google.com by [email protected]
on 3 Jul 2013 at 12:19
1. mutliple views
2. switch to per vertex color
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:35
What steps will reproduce the problem?
1. Display point or vector glyphs on surface
2. Increase primitive size using slider
3. Decrease primitive size using slider --> primitive size on glyphs gets stuck
at a higher value than the slider is positioned at and requires a bit of
fiddling to get it back to normal
- Seems to be dependent on how fast I move the slider (i.e. doesn't happen if I
move the slider really slowly)
Original issue reported on code.google.com by [email protected]
on 15 Jul 2013 at 2:18
brainGL crashes when I check the 'render colormap' option in the colormap tab.
Original issue reported on code.google.com by [email protected]
on 14 Nov 2013 at 12:54
We need full cortical surface background under the glyphs.
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:16
What steps will reproduce the problem?
1. load surface with values (e.g glyphset)
2. lower/upper threshold slider works normaly
3. after changing min / max slider, lower/upper threshold slider get blocked
What is the expected output? What do you see instead?
- no interaction with min/max slider as on startup
What version of the product are you using? On what operating system?
1160:ac62ebd1935b
Original issue reported on code.google.com by [email protected]
on 16 Jan 2014 at 8:26
Loading an additional .set file for painting on the surface in main gl blocks
the view of the surface connectivity map in main GL 2.
To reproduce:
1. Load an anatomical nifiti file and associated glyphset
2. Configure parameters to show glyphs on plain surface mesh in main gl and
"vertex data" connectivity map in main GL 2
3. Load in an additional .set surface file (for drawing ROIs on the surface)
The new surface shows up in main GL 2 and blocks the visibility of the
seed-based connectivity map
Suggestion:
Make it possible to choose whether additional datasets such as .set files
appear in one or both views.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 9:57
It would be very helpful to have some form of crosshairs on the brain surface
to indicate where you have clicked when comparing areas in two views. Ideally,
something similar to the crosshairs in suma would be great.
Original issue reported on code.google.com by [email protected]
on 5 Jul 2013 at 8:08
It would be useful (and really cool!) to be able to use a slider to change the
'inflatedness' of the brain surface instead of switching between pial,
inflated, very inflated etc.
Original issue reported on code.google.com by [email protected]
on 15 Jul 2013 at 2:26
What steps will reproduce the problem?
1. create new dataset ( e.g.gauss filtering )
2. save file or scene
3. no filename suggestion
What is the expected output? What do you see instead?
Save with the name of the dataset.
What version of the product are you using? On what operating system?
Linux - Current
Original issue reported on code.google.com by [email protected]
on 19 Nov 2013 at 9:31
What steps will reproduce the problem?
1. load data set
2a. load vtk polydata file
2b. load another vtk polydata file
3. set mesh color to some green
4. change alpha of mesh object (0.26)
5. menu -> Help -> Screenshot
What is the expected output? What do you see instead?
- It should look like on the screen
- Mesh object is partly black
What version of the product are you using? On what operating system?
- latest
- Linux
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 24 May 2013 at 3:22
Having some display of differences between neighboring glyphs shown at the
midpoint between two nodes. Could either show the actual differences in the
connectivity profile (e.g. a shift in a specific region) or could be a
representation of the degree of similarity/difference between them (e.g.
something like a pie chart that gets bigger the higher the difference is).
Original issue reported on code.google.com by [email protected]
on 15 Jul 2013 at 2:34
Sometimes taking a screenshot through braingl causes the main gl graphics to
mess up completely, requiring a restart of the program.
Original issue reported on code.google.com by [email protected]
on 20 Aug 2013 at 9:28
What steps will reproduce the problem?
1.loading a functional dataset
2.creating an isosurface
3.trying to show only the isosurface in maingl1 and only the slices in maingl 2
What is the expected output? What do you see instead?
whenever i toggle the slices they switch on and off for both views (though i
try ctrl+klick the toolbar buttons)
Please use labels and text to provide additional information.
Original issue reported on code.google.com by [email protected]
on 15 Nov 2013 at 12:32
Since the rendering of colormaps is currently broken, can we hide the property
tab for that thing?
Original issue reported on code.google.com by [email protected]
on 24 Oct 2013 at 3:43
Please setup importing from mrtrix and trackvis file formats.
Cheers,
Chris
(data files in scr/alaska1/2uFromSteele/braingl
data_CSD_tracked_determ - mrtrix format (only 100 tracks, not pretty at all,
will put a nicer one with 1000 tracks in there when it finishes)
I will also place a trackvis version of the file there shortly.
Cheers,
Chris
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 9:54
I would be really helpful to have an additional 'medial view' button next to
the axial, coronal, and sagittal ones. i.e. so that the medial wall of the
cortical surface is facing the user without having to rotate it manually and
screw up the sagittal alignment.
Original issue reported on code.google.com by [email protected]
on 24 Jul 2013 at 8:25
Deleting datasets does not free all the arrays
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:37
What steps will reproduce the problem?
1. load glpyhset dataset
2. raise threshold and minimum length high enough so no glyphs remain
3. click make new connections
What is the expected output? What do you see instead?
no crash / crash
Original issue reported on code.google.com by [email protected]
on 8 Jul 2013 at 9:21
What steps will reproduce the problem?
1. Make new colormap (save as new in colormap editor)
2. Try to use that in the currently selected dataset
3. It's not there...
What is the expected output? What do you see instead?
The new colormaps only show up for newly loaded datasets, or after changing the
selection
Original issue reported on code.google.com by [email protected]
on 24 Oct 2013 at 3:39
It would also be nice to be able to run braingl from the command line to do
some track thinning and/or downsampling of data.
This would be very useful for very large datasets!
e.g.
braingl -trckthin -rate 1/10 <in> <out>
Cheers,
Chris
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 9:57
What steps will reproduce the problem?
1. load file
2. make transparent
3. ...
4. profit
Original issue reported on code.google.com by [email protected]
on 26 Apr 2013 at 7:29
What steps will reproduce the problem?
1. Load fa and CSD ODF data.
2. The glyphs are not shown in the voxels but at the corners of the voxel.
What is the expected output? What do you see instead?
ODF in the middle of the voxel.
What version of the product are you using? On what operating system?
current.
Original issue reported on code.google.com by [email protected]
on 7 Mar 2014 at 2:15
Attachments:
What steps will reproduce the problem?
1. load MR (1mm)
2. distance map - isosurface
3. paint in volume by drawing on the surface (brush size 1)
What is the expected output? What do you see instead?
- The marked ROI should follow the surface. Instead, not all voxels are marked.
- The drawn positions are shifted ( seed attached picture )
What version of the product are you using? On what operating system?
- version 1190:9e24eec59894 - Linux
Original issue reported on code.google.com by [email protected]
on 3 Mar 2014 at 5:17
Attachments:
The use of ROIs isn't yet described. The description in list of GUI views
references to the "displayable datatypes" page but there is no further
information on ROIs.
Original issue reported on code.google.com by [email protected]
on 28 Oct 2013 at 9:27
The surface crosshairs only appear when a glyphset with connectivity data is
loaded, and not when a surface set is loaded on its own. The crosshairs also
disappear if both a glyphset and a surface set are loaded, and you then switch
off the visibility of the glyphset.
To reproduce:
Load a nifti, glyphset, and surface set. Toggle visibility of glyphset and
notice that crosshairs toggle on and off too.
Original issue reported on code.google.com by [email protected]
on 20 Jan 2014 at 9:39
The "save scene" option only saves certain parameters of main GL 1. It would be
even more useful if it would also save parameters for main GL 2, and also
parameters related to the glyph representations. This would save a lot of time
reconfiguring parameters when reopening a dataset.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 10:34
What steps will reproduce the problem?
1. load 10 textures
2. swich textures "on" and "off"
3. memory load increases
What is the expected output? What do you see instead?
Constant memory.
What version of the product are you using? On what operating system?
Current - Linux
Original issue reported on code.google.com by [email protected]
on 19 Nov 2013 at 9:57
Looks like somebody did break something after all! ;)
Crashes when I load a nifti file and then click any of the three buttons to
align the brain (the second set of the three little axial/sagittal/coronal
slice buttons).
Original issue reported on code.google.com by [email protected]
on 17 Jul 2013 at 2:04
In the save menu, if you don't specify a file extension, braingl will save with
the extension .vtk, regardless of whick file type is selected in the filter
menu below.
To reproduce:
1. Open a dataset (only tested with surface/glyphsets)
2. Open the save menu and select a file type other than .vtk from the filter
menu
3. Save the file without typing a file extension
4. Navigate to your saved file
--> The extension .vtk is added to your saved file
It would also be useful if brainGL automatically added the extension that is
selected in the filter.
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 10:39
The 'render colormap' option only works when a glyphset with connectivity data
is loaded, and not when a surface set is loaded on its own. The colorbar also
disappears when you switch off the visibility of the glyphset.
To reproduce:
Load a nifti, glyphset, and surface set. Toggle visibility of glyphset and
notice that the colorbar toggles on and off too.
Original issue reported on code.google.com by [email protected]
on 20 Jan 2014 at 9:43
It would be really helpful if the zoom option centered on wherever the
crosshairs are positioned (i.e. you click on an area of interest and when you
zoom, that area will be in the center of the window)
Original issue reported on code.google.com by [email protected]
on 20 Aug 2013 at 9:01
BrainGL crashes (after a few seconds) when you delete a glyphset from the
dataset list.
To reproduce:
1. Load an anatomical nifti volume
2. Load an associated glyphset
3. Delete the glyphset from the dataset list
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 9:52
What steps will reproduce the problem?
1. Load anatomie and 6 rois
2. Only 4 roi's are visible
What is the expected output? What do you see instead?
All textures visible or at least feedback indicating which textures are shown
What version of the product are you using? On what operating system?
Linux - Current
Original issue reported on code.google.com by [email protected]
on 19 Nov 2013 at 9:41
Steps to reproduce the error:
1. Turn off glyphs
2. Switch surface
Original issue reported on code.google.com by [email protected]
on 2 Jul 2013 at 4:20
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.