fsleyes issueshttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues2021-04-08T11:33:22+01:00https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/78Fix synced movie mode on all platforms2021-04-08T11:33:22+01:00Paul McCarthyFix synced movie mode on all platformsMovie mode involves [some hacks](fsleyes/views/canvaspanel.py#L808) on certain graphics cards. Try and make it work in a synchronised manner on all platforms.Movie mode involves [some hacks](fsleyes/views/canvaspanel.py#L808) on certain graphics cards. Try and make it work in a synchronised manner on all platforms.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/86Edit mode: Grow/erode selection2019-10-08T13:26:19+01:00Paul McCarthyEdit mode: Grow/erode selectione.g. if you would like to grow/erode a maske.g. if you would like to grow/erode a maskPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/81Clipping range is off under linux/VM2017-06-11T18:02:13+01:00Paul McCarthyClipping range is off under linux/VMNot sure if it is a linux issue or a VM issue.
When loading the MNI152 1 or 2mm templates, it seems that voxels with a value of zero are only clipped when the low clipping range is set to 128.Not sure if it is a linux issue or a VM issue.
When loading the MNI152 1 or 2mm templates, it seems that voxels with a value of zero are only clipped when the low clipping range is set to 128.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/69Group analysis browser2019-05-14T09:40:49+01:00Paul McCarthyGroup analysis browserA control panel which allows easy navigation of (e.g.) FEAT group analyses.
Thoughts:
- A prompt which allows the user to type in a file system path (with tab completion)
- A list which shows the contents of the current path (with th...A control panel which allows easy navigation of (e.g.) FEAT group analyses.
Thoughts:
- A prompt which allows the user to type in a file system path (with tab completion)
- A list which shows the contents of the current path (with thumbnails for `.nii` images, and maybe `.feat`/`.ica` directories)
- The ability to filter this list according to a wildcard
- The ability to recurse into sub-directories, and list all files which match a wildcard patternFSLeyes 1.0.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/58Slice-wise histogram2017-10-01T15:12:02+01:00Paul McCarthySlice-wise histogramWould it be useful if the ``HistogramPanel`` were able to add histograms for individual slices from an ``Image`` overlay?Would it be useful if the ``HistogramPanel`` were able to add histograms for individual slices from an ``Image`` overlay?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/57FEATInfo control panel2017-10-01T15:12:02+01:00Paul McCarthyFEATInfo control panelA control panel which shows information about the FEAT analysis (if a ``FEATImage`` is selected). Could show things like:
- the design matrix
- contrasts
- efficiency matrix
- results
- ...A control panel which shows information about the FEAT analysis (if a ``FEATImage`` is selected). Could show things like:
- the design matrix
- contrasts
- efficiency matrix
- results
- ...Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/55Editor: limit selection by intensity2017-10-01T15:12:02+01:00Paul McCarthyEditor: limit selection by intensityAdd the ability to select all voxels above/below a specified intensity. Perhaps just a range setting, which applies to all selections?Add the ability to select all voxels above/below a specified intensity. Perhaps just a range setting, which applies to all selections?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/54LightBoxPanel: Ability to specify exactly which slices are displayed2019-10-17T17:05:30+01:00Paul McCarthyLightBoxPanel: Ability to specify exactly which slices are displayedThe slice range and slice spacing options are a bit too simplistic and clunky. While you could keep these interface widgets the same, internally it might be easier to maintain an explicit list (in display space coordinates) of the slices...The slice range and slice spacing options are a bit too simplistic and clunky. While you could keep these interface widgets the same, internally it might be easier to maintain an explicit list (in display space coordinates) of the slices that are to be displayed.
This could also be an advanced option exposed to the user somehow.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/53Editor: Honour clipping range2017-10-01T15:12:02+01:00Paul McCarthyEditor: Honour clipping rangeThe editor should honour the clipping range of the image being edited - clipped voxels should not be selected.
Or would this be too confusing?The editor should honour the clipping range of the image being edited - clipped voxels should not be selected.
Or would this be too confusing?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/52Editor: Support for 4D2017-10-01T15:12:02+01:00Paul McCarthyEditor: Support for 4DThe editor should have the ability to apply changes (fill, mask, ROI) to all images in a 4D volume.The editor should have the ability to apply changes (fill, mask, ROI) to all images in a 4D volume.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/51HistogramPanel: Support for 4D2017-10-01T15:12:02+01:00Paul McCarthyHistogramPanel: Support for 4DShould the HistogramPanel have more support for 4D? For example, when a histogram is added for a 4D image, the user could be prompted to choose one of
- Histogram for current volume
- Histogram across all volumes
- Histogram for e...Should the HistogramPanel have more support for 4D? For example, when a histogram is added for a 4D image, the user could be prompted to choose one of
- Histogram for current volume
- Histogram across all volumes
- Histogram for every volumePaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/105Make classification panel work with overlays2018-02-05T14:49:12+00:00Paul McCarthyMake classification panel work with overlaysClassification panel currently only works with 4D images. Make it work with all loaded overlays too. For the classification panel to work, you just need:
- A number (number of things to be classified - volumes of a 4D image, or loaded ...Classification panel currently only works with 4D images. Make it work with all loaded overlays too. For the classification panel to work, you just need:
- A number (number of things to be classified - volumes of a 4D image, or loaded overlays)
- Event handlers to change the current thing when the row in the classification panel changes, and vice versa.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/109Change all logging calls so they don't format strings2018-03-14T14:00:19+00:00Paul McCarthyChange all logging calls so they don't format stringsCurrently all logging calls in FSLeyes (and associated projects) call `.format` on the log string, e.g.:
```
log.debug('format this string: {} {} {}'.format('a', 'b', 'c'))
```
But the `logging` module can do string formatting for us:
...Currently all logging calls in FSLeyes (and associated projects) call `.format` on the log string, e.g.:
```
log.debug('format this string: {} {} {}'.format('a', 'b', 'c'))
```
But the `logging` module can do string formatting for us:
```
log.debug('format this string: {} {} {}', 'a', 'b', 'c')
```
If you switch over to this convention, it will mean that there does not have to be a (large) performance penalty to leaving log calls in the code.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/115"Processing" control panel2018-04-25T09:11:53+01:00Paul McCarthy"Processing" control panel1. Have options to run tasks, e.g. `bet`, `fnirt`, `flirt`.
2. Whenever user runs a task, add it to an internal list of running tasks.
3. The "Processing" control panel has a list of running/past tasks, and their statuses (e.g. still r...1. Have options to run tasks, e.g. `bet`, `fnirt`, `flirt`.
2. Whenever user runs a task, add it to an internal list of running tasks.
3. The "Processing" control panel has a list of running/past tasks, and their statuses (e.g. still running, finished, crashed.). Users can select a task from the list, and view stdout/stderr.
4. When task has finished, ability to view outputs in FSLeyes.
- hrefs to arguments in command string?
- Identify which arguments to wrapper function have a value of `LOAD` (see `fsl.wrappers`)?
You could either wrap, or monkey-patch the `fsl.wrappers` functions to intercept task invocations, so they can be managed and queried.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/117Save/load full FSLeyes state2018-05-19T17:42:47+01:00Paul McCarthySave/load full FSLeyes stateA file/directory format that can reproduce the full FSLeyes state (layout and overlays).
Menu options:
- *File -> Load FSLeyes specification*
- *File -> Save FSLeyes specification*
Specification is a file (possibly within a director...A file/directory format that can reproduce the full FSLeyes state (layout and overlays).
Menu options:
- *File -> Load FSLeyes specification*
- *File -> Save FSLeyes specification*
Specification is a file (possibly within a directory called `[myspec].fsleyes/`), containing:
- File version
- Portable/non-portable flag
- State string (see `fsleyes.state.getState`):
If portable, alongside the spec file are all overlays and vertex data files, renamed to be minimally unique.
*Load FSLeyes specification* asks user for spec file.
*Save FSLeyes specification* asks user:
- Make spec portable?
- If non-portable:
- ask for file name.
- just save spec file with full paths to overlays
- if portable:
- ask for directory name
- Ask for which overlays to include (default to all)
- Generate minimally unique names for included overlays/data files
- Generate state with new overlay/data file names
- Copy all overlays/data files into directory
- Save spec file into directory, using relative path namesPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/1183D FOD display2018-06-04T11:00:12+01:00Paul McCarthy3D FOD displayFor SH overlays, in the 3D view, display the FOD at the current voxel location.For SH overlays, in the 3D view, display the FOD at the current voxel location.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/45Turn on spline interpolation for images in 'affine' space2018-08-18T01:35:57+01:00Paul McCarthyTurn on spline interpolation for images in 'affine' spaceThis was previously done by the OverlayDisplayPanel, but now that GEDMode (issue fsl/fslpy#19) has been implemented, it no longer makes sense to do it there.
Could be done either in the DisplayContext (ugh), or perhaps I can think of a ...This was previously done by the OverlayDisplayPanel, but now that GEDMode (issue fsl/fslpy#19) has been implemented, it no longer makes sense to do it there.
Could be done either in the DisplayContext (ugh), or perhaps I can think of a cleaner way to implement it, and to implement similar types of dependent behaviour.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/44Transfer editor selection between images2018-08-18T01:35:57+01:00Paul McCarthyTransfer editor selection between imagesIt could be useful in edit mode to allow a selection to be transferred between images. This feature was present pre-GEDMode, but it was a hack. The selection mask from the source image should be properly transformed, interpolated, and re...It could be useful in edit mode to allow a selection to be transferred between images. This feature was present pre-GEDMode, but it was a hack. The selection mask from the source image should be properly transformed, interpolated, and resampled, into the space of the destination image.
This could be an edit toolbar button which pops up a dialog prompting the user to select the destination image and some basic interpolation options.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/43Multiple selection in overlay list2018-08-18T01:35:57+01:00Sean FitzgibbonMultiple selection in overlay listThis could be in addition to, or instead of, the link option for grouping overlays. It might be more intuitive and require less clicks....This could be in addition to, or instead of, the link option for grouping overlays. It might be more intuitive and require less clicks....Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/42Brain anatomy quiz mode2018-08-18T01:35:57+01:00Gerard RidgwayBrain anatomy quiz modeI suggest adding a flash-card style neuroanatomy quiz feature, in which the viewer would launch showing one of the standard templates (probably MNI152_T1_1mm) and the user would select one of the reasonable atlases (i.e. anything but Tal...I suggest adding a flash-card style neuroanatomy quiz feature, in which the viewer would launch showing one of the standard templates (probably MNI152_T1_1mm) and the user would select one of the reasonable atlases (i.e. anything but Talairach). Then the user would select either of the following modes:
* Identify location -- Crosshair jumps to centre of random region (from selected atlas), presents multiple choice question with correct region name among five randomly ordered region names (either completely randomly chosen, or perhaps choose closest regions, if not too slow to identify these). Move to new region once correct answer is clicked.
* Find region -- Random region is named, user must try to locate crosshair inside region, click "submit" when done. If correct, show region in overlay, allow user to click "next"; if incorrect, indicate distance from region centre, allow user to try again or to choose "show me" (then to click "next" once happily educated).
Optional feature to keep track of success rate, e.g. showing percent correct-first-time, over all "games" and just over last 5 games. ~~Percentage too low results in automatic disciplinary action.~~Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/40Make profiles configurable2018-08-18T01:35:57+01:00Paul McCarthyMake profiles configurableFeatures such as changing the current slice via the scroll-wheel should be able to be enabled/disabled. Options like this could be added as a group of controls in the view settings panel.
In the long term, it would be nice to allow the ...Features such as changing the current slice via the scroll-wheel should be able to be enabled/disabled. Options like this could be added as a group of controls in the view settings panel.
In the long term, it would be nice to allow the user full control over mouse/modifier key behaviour - a separate config panel?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/37'Slicesdir'-style view2018-08-18T01:35:57+01:00Paul McCarthy'Slicesdir'-style viewIt might be useful to add a new view panel which gives a display similar to ``slicesdir``, i.e. allows the user to quickly view and compare lots of overlays.It might be useful to add a new view panel which gives a display similar to ``slicesdir``, i.e. allows the user to quickly view and compare lots of overlays.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/36Context menu with copy option in Overlay info panel and Location panel2018-08-18T01:35:57+01:00Paul McCarthyContext menu with copy option in Overlay info panel and Location panelIn the ``OverlayInfoPanel`` and ``LocationPanel`` (both using ``wx.html.HtmlWindow`` widgets), users can select text and copy it using CTRL+C (or CMD+C). But it would be nice to have a right-click context menu with a copy option. I thoug...In the ``OverlayInfoPanel`` and ``LocationPanel`` (both using ``wx.html.HtmlWindow`` widgets), users can select text and copy it using CTRL+C (or CMD+C). But it would be nice to have a right-click context menu with a copy option. I thought that wx would do this by default, but it evidently doesn't.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/35Specify melodic label file on command line2018-08-18T01:35:57+01:00Paul McCarthySpecify melodic label file on command lineAbility to specify a melodic_IC file (or .ica dir), and an associated label file to use, on the command line.Ability to specify a melodic_IC file (or .ica dir), and an associated label file to use, on the command line.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/34Better management of texture resources2018-08-18T01:35:57+01:00Paul McCarthyBetter management of texture resourcesThe texture resource naming convention is ad-hoc, and large texture resources are not shared as much as they could be.
Texture resources should be accessed by their properties (e.g. the image itself, resolution, interpolation, etc), so ...The texture resource naming convention is ad-hoc, and large texture resources are not shared as much as they could be.
Texture resources should be accessed by their properties (e.g. the image itself, resolution, interpolation, etc), so that different things which need an equivalent texture will naturally end up sharing the same texture, instead of creating a duplicate.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/31Re-factor props/syncable functionality.2018-08-18T01:35:57+01:00Paul McCarthyRe-factor props/syncable functionality.(This is a ``props`` issue).
The parent-child relationships between DisplayContexts, Displays, and DisplayOpts is continuing to be a cause of bugs and kludgy workarounds.
Both parent and child instances register listeners on themselve...(This is a ``props`` issue).
The parent-child relationships between DisplayContexts, Displays, and DisplayOpts is continuing to be a cause of bugs and kludgy workarounds.
Both parent and child instances register listeners on themselves, but parent instances are really only necessary for property value synchronisation.
The ``syncable`` module should be re-written (or a new module written) which just proivides synchronisation capability. A solution similar to the ``fsl.fsleyes.group`` module might work.
Another thing ... I would like to be able to run ``FSLeyes`` (or parts thereof) without having to create a hierarchy of DisplayContexts (and associated classes).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/30Overlay blending2018-08-18T01:35:57+01:00Paul McCarthyOverlay blendingHave a look at how the colours of transparent overlays are blended.
For example, if we have two mask overlays, one yellow and one blue, both at 50%, shouldn't the mask intersection be the same colour (hopefully a shade of green), no ma...Have a look at how the colours of transparent overlays are blended.
For example, if we have two mask overlays, one yellow and one blue, both at 50%, shouldn't the mask intersection be the same colour (hopefully a shade of green), no matter what the order?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/120Jupyter notebook misbehaving under VNC2018-08-30T16:40:38+01:00Paul McCarthyJupyter notebook misbehaving under VNCIn Fidel's VNC session on jalapeno18, firefox didn't open, and the `screenshot` function produced corrupt resultsIn Fidel's VNC session on jalapeno18, firefox didn't open, and the `screenshot` function produced corrupt resultsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/29Mask intersection overlay2018-11-08T22:15:08+00:00Paul McCarthyMask intersection overlayPotentially useful feature: a new overlay type, a 'mask container' which allows the user to add mask images to it, and control how the intersection of the different masks are coloured.
Slightly related: fsl/fslpy#136Potentially useful feature: a new overlay type, a 'mask container' which allows the user to add mask images to it, and control how the intersection of the different masks are coloured.
Slightly related: fsl/fslpy#136Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/25Real time tractography display?2018-11-08T22:15:08+00:00Paul McCarthyReal time tractography display?Choose a location, and display (pre-calculated) probabilistic tractography resultsChoose a location, and display (pre-calculated) probabilistic tractography resultsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/127More ortho layouts2019-11-06T03:35:15+00:00Paul McCarthyMore ortho layoutsOption to display one major, and two minor canvases. e.g.:
```
+------+---+
| |cor|
|axial +---+
| |sag|
+------+---+
```Option to display one major, and two minor canvases. e.g.:
```
+------+---+
| |cor|
|axial +---+
| |sag|
+------+---+
```FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/22Plot motion parameters in Melodic mode2019-03-19T14:54:36+00:00Paul McCarthyPlot motion parameters in Melodic modeIf motion parameters have been estimated for a melodic data set, it would be useful to be able to plot them in the time series panel, along with component time courses. Related to fsl/fslpy#32If motion parameters have been estimated for a melodic data set, it would be useful to be able to plot them in the time series panel, along with component time courses. Related to fsl/fslpy#32Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/21'Remove trimmings' option2019-03-19T14:54:36+00:00Paul McCarthy'Remove trimmings' optionWhen setting up FSLeyes for more complicated screen shots (e.g. lightbox + time series + power spectrum), it would be useful to toggle on/off all window decorations (scrollbars, title bars, etc etc).When setting up FSLeyes for more complicated screen shots (e.g. lightbox + time series + power spectrum), it would be useful to toggle on/off all window decorations (scrollbars, title bars, etc etc).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/20RIght click on a view panel should show the view panel menu2019-03-19T14:54:36+00:00Paul McCarthyRIght click on a view panel should show the view panel menuAllow view panel menu to be accessed via a right-click context menu popup.Allow view panel menu to be accessed via a right-click context menu popup.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/17specifying intensity threshold for voxel selection in edit mode2019-03-19T14:54:36+00:00Lennart Verhagenspecifying intensity threshold for voxel selection in edit modeI encountered a few issues with specifying the intensity threshold for intensity-based voxel selection in edit mode. I really like the edit mode, and this specific selection type is a nice addition. Please see all my comments as very min...I encountered a few issues with specifying the intensity threshold for intensity-based voxel selection in edit mode. I really like the edit mode, and this specific selection type is a nice addition. Please see all my comments as very minor and friendly suggestions. When I initially enter this mode the intensity threshold is set at 10, regardless of the intensities in the actual image. For example I wanted to select voxels from an FA image. I also noticed that the down-button had no effect, I could only press "up" to go higher than 10. I could mouse-scroll, but this took a very long scroll to values below 1. The scroll speed is not dependent on the value (nor the arrow jump), so once I got below 1 it was nearly impossible to select an appropriate value between 0 and 1 with the mouse scroll. Adjusting the intensity value does not adjust the current intensity-selection, you have to click to do this again. I ended up with a set of multiple erroneous selections, so I had to clear all selections, and do it again. I see that this is a compromise, but to me an intuitive workflow would be that I make an intensity-based selection (by mouse selection), see that is it too big/small, and adjust the threshold (requiring you to move your mouse cursor away from the selection). It isn't always easy to have to move your cursor back to your initial voxel.https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/16Reset range to current volume2019-03-19T14:54:36+00:00Paul McCarthyReset range to current volumeOn display toolbar, for volume overlays, a button which allows the user to adjust the display/clipping range to the range of the current volume.On display toolbar, for volume overlays, a button which allows the user to adjust the display/clipping range to the range of the current volume.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/15Merge mask images2019-03-19T14:54:36+00:00Paul McCarthyMerge mask imagesWhen creating mask images it might be useful to allow multiple masks to be merged e.g. via union or intersection (or addition/subtraction, if a non-binary mask).When creating mask images it might be useful to allow multiple masks to be merged e.g. via union or intersection (or addition/subtraction, if a non-binary mask).Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/13Optimise seed correlation2019-03-19T14:54:36+00:00Paul McCarthyOptimise seed correlationIt's slow and force-loads the entire image (which is possibly why it is slow). Fix these things.It's slow and force-loads the entire image (which is possibly why it is slow). Fix these things.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/11Atlas panel - load affine/nonlinear transformation to query non-MNI152 images?2019-03-19T14:54:36+00:00Paul McCarthyAtlas panel - load affine/nonlinear transformation to query non-MNI152 images?Why don't we just build `Featquery_gui` into FSLeyes?Why don't we just build `Featquery_gui` into FSLeyes?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/9IC label panel sync and focus2019-03-19T14:54:36+00:00Paul McCarthyIC label panel sync and focusWhen you select a tag in the label grid, the volume should be displayed
Focus of the specific tag should be retained .... although this might be complicatedWhen you select a tag in the label grid, the volume should be displayed
Focus of the specific tag should be retained .... although this might be complicatedPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/6Contour overlay2019-03-19T14:54:36+00:00Paul McCarthyContour overlay1. Coloured according to a `LookupTable` which defines the contour values
2. Use a technique based on the `VolumeOpts.colourMapResolution` setting to draw the contours
3. Option to draw contour lines, or contour bands1. Coloured according to a `LookupTable` which defines the contour values
2. Use a technique based on the `VolumeOpts.colourMapResolution` setting to draw the contours
3. Option to draw contour lines, or contour bandsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/5CIFTI overlays2019-11-06T03:34:42+00:00Paul McCarthyCIFTI overlaysWhat it says on the tin.What it says on the tin.FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/2props: remove attribute listeners?2019-03-19T14:54:36+00:00Paul McCarthyprops: remove attribute listeners?Is a distinction between property value listeners and property attribute listeners necessary?Is a distinction between property value listeners and property attribute listeners necessary?Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/1DisplayOpts mixin classes2019-03-19T14:54:36+00:00Paul McCarthyDisplayOpts mixin classesSimilar to the `ColourMapOpts` class, you should also add a `4DOpts` (with a better, less syntactically invalid name) class for overlay types which may be 4D, and a `LutOpts` class for overlay types with lookup tables.
This will allow ...Similar to the `ColourMapOpts` class, you should also add a `4DOpts` (with a better, less syntactically invalid name) class for overlay types which may be 4D, and a `LutOpts` class for overlay types with lookup tables.
This will allow you to remove explicit handling of different overlay types in e.g. the location panel (the volume counter), and the lookup table panel.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/145ability to edit multi-channel images2019-09-06T08:54:04+01:00Paul McCarthyability to edit multi-channel imagesPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/167filetree: load notes column from file2019-12-02T10:53:26+00:00Paul McCarthyfiletree: load notes column from fileAssume that user has configured filetree grid appropriately, then load the `Notes` column (or allow a single-column plain text file)Assume that user has configured filetree grid appropriately, then load the `Notes` column (or allow a single-column plain text file)FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/168Copy geometry menu option2019-12-02T10:53:40+00:00Paul McCarthyCopy geometry menu optionThe FSLeyes equivalent of `fslcpgeom`The FSLeyes equivalent of `fslcpgeom`FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/170apply flirt dialog uses wrong reference2019-12-02T10:54:00+00:00Paul McCarthyapply flirt dialog uses wrong referenceThe apply flirt transform dialog uses file names to uniquely identify which reference image to use. This doesn't work when the same image is loaded twice (e.g. MNI152_T1_2mm), and one of them has been "nudged" - the wrong refernce may be...The apply flirt transform dialog uses file names to uniquely identify which reference image to use. This doesn't work when the same image is loaded twice (e.g. MNI152_T1_2mm), and one of them has been "nudged" - the wrong refernce may be selected.FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/171New image option: choose nifti1/nifti22019-12-02T10:54:12+00:00Paul McCarthyNew image option: choose nifti1/nifti2_New image_ currently always outputs nifti2. Maybe an option to choose nifti1 or nifti2?
The default value for the option could be based on the FSL version, and/or the value of `$FSLOUTPUTTYPE`_New image_ currently always outputs nifti2. Maybe an option to choose nifti1 or nifti2?
The default value for the option could be based on the FSL version, and/or the value of `$FSLOUTPUTTYPE`FSLeyes 0.33.0Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/174command line flag to automatically assign colour maps2019-12-21T02:00:01+00:00Paul McCarthycommand line flag to automatically assign colour mapse.g. this:
```
fsleyes --auto_colourmap -std mask1 mask2 mask3
```
would be equivalent to this:
```
fsleyes -std mask1 -cm red mask2 -cm blue mask3 -cm green
```
And/or perhaps a flag which sets all overlays to masks, and colours them ...e.g. this:
```
fsleyes --auto_colourmap -std mask1 mask2 mask3
```
would be equivalent to this:
```
fsleyes -std mask1 -cm red mask2 -cm blue mask3 -cm green
```
And/or perhaps a flag which sets all overlays to masks, and colours them differentlyPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/175warn when pixdims don't match affine2020-01-23T16:04:44+00:00Paul McCarthywarn when pixdims don't match affineif pixdims don't match affine, an image will be displayed differently when it is set as the display space - in this case, a scaling matrix is constructed from the pixdims. In other cases, the sform is used. This suggests that the image h...if pixdims don't match affine, an image will be displayed differently when it is set as the display space - in this case, a scaling matrix is constructed from the pixdims. In other cases, the sform is used. This suggests that the image header may be invalid, so maybe a warning should be displayed.Paul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/206print outputs are directed to console when run from jupyter notebook2023-02-10T10:04:54+00:00Paul McCarthyprint outputs are directed to console when run from jupyter notebookhttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/208Make "Modulate alpha by intensity" pos/neg aware2023-06-07T15:07:36+01:00Tom NicholsMake "Modulate alpha by intensity" pos/neg awareThe "Modulate alpha by intensity" *almost* allows users to do the AFNI-recommended visualisation of %BOLD/units values modulated by a statistic map. What is missing is easy visualisation of both positive and negative values (which is pa...The "Modulate alpha by intensity" *almost* allows users to do the AFNI-recommended visualisation of %BOLD/units values modulated by a statistic map. What is missing is easy visualisation of both positive and negative values (which is part of the recommendation).
Suggestion: Make the modulation follow according to the *absolute* *value* of the (alpha) source image... either optionally *or* as linked to the use of activation of the negative color map on the source image.
As another suggestion, you might make your life easier if you remove the "modulate range" sliders from the Overlay Display Settings, and simply take the range from the display range of the source image. In this way, when there is only a positive color bar, you can map alpha by the Min/Max display range; and when negative color bar is activated, map alpha from abs(source).
Ref: Taylor, P. A., Reynolds, R. C., Calhoun, V., Gonzalez-Castillo, J., Handwerker, D. A., Bandettini, P. A., … Chen, G. (2023). Highlight results, don’t hide them: Enhance interpretation, reduce biases and improve reproducibility. NeuroImage, 274(October 2022), 120138. https://doi.org/10.1016/j.neuroimage.2023.120138https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues/209Histogram suggestions2023-07-20T09:36:20+01:00Tom NicholsHistogram suggestionsHaving used the histogram tool intenseively in the last day or so I noticed a few quirks that, while are all very low priority, I thought I'd mention them:
1. The location of the legend is always upper right, and that sometimes can be e...Having used the histogram tool intenseively in the last day or so I noticed a few quirks that, while are all very low priority, I thought I'd mention them:
1. The location of the legend is always upper right, and that sometimes can be exactly where the action is in a plot; a way to move it to top left or other location would be great.
2. The legend and line color/style order seems to be fixed, I think alphebetical. It would be nice if that order could be changed, e.g. corresponding to the order in the overlay list.
3. In the Settings panel, under "Histogram settings for <<image>>" there are data range parameters that would be useful to set globally for all iamges, e.g., at least number of bins & data range. As another low pripority suggestion, maybe have an option to 'lock' all of them to have shared settings, so the number of bins was set for all (e.g. I'm showing histograms for 5 different images, and I didn't notice that the bottom section was image specific, and set the bin count once thinking it applied to all).
That's it! Just food for thought.