theprojecter / braingl Goto Github PK

It would be helpful to provide a link to the web documentation in the "Help" 
menu

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.

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)

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.

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)

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.

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.

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.

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.

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. 

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.

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

Sometimes taking a screenshot through braingl causes the main gl graphics to 
mess up completely, requiring a restart of the program.

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.

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

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.

High priorities:

-color mapping of the surface
-visibility of stuff

-more general solution later

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

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

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).

copied fibers need to retain their extra values
saving/loading needs to keep extra data intact

We need full cortical surface background under the glyphs.

-Using the color maps into the connectivity values
-constant color
-coordinates instead of direction

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...

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

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.

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.

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

Deleting datasets does not free all the arrays

Steps to reproduce the error:

1. Turn off glyphs
2. Switch surface

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.

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.

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

Since the rendering of colormaps is currently broken, can we hide the property 
tab for that thing?

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

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

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.

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

brainGL crashes when I check the 'render colormap' option in the colormap tab.

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.

1. mutliple views
2. switch to per vertex color

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.

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.

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.

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.

What steps will reproduce the problem?
1. load file
2. make transparent
3. ...
4. profit

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).

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

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

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)