fsleyes issueshttps://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/issues2019-12-02T10:53:26+00:00https://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/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.https://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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 McCarthy