DIVE issueshttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues2022-11-07T09:13:34+00:00https://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/113Current package incompatibility2022-11-07T09:13:34+00:00William ClarkeCurrent package incompatibilityjinja2 (>3.1?) changed its import API breaking panel <0.12.7. See https://github.com/holoviz/panel/issues/3257.
When I ran `pip install .` I got an incompatible selection of packages with panel 12.1 and jinja2 3.1.x. You might need to p...jinja2 (>3.1?) changed its import API breaking panel <0.12.7. See https://github.com/holoviz/panel/issues/3257.
When I ran `pip install .` I got an incompatible selection of packages with panel 12.1 and jinja2 3.1.x. You might need to pip panel >12.7 in the setup.https://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/110fix text case2021-09-02T10:28:35+01:00Saad Jbabdifix text caseAt the moment some of the text starts with capital letters and some doesn't. This needs fixing.At the moment some of the text starts with capital letters and some doesn't. This needs fixing.Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/109describe pre-baked models in readme2021-09-03T13:24:47+01:00Hossein Rafipoordescribe pre-baked models in readmeAdd a section for prebaked models that is a list of the models and the references.Add a section for prebaked models that is a list of the models and the references.Hossein RafipoorHossein Rafipoorhttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/104Signal either SMT or along orientation2021-08-04T08:37:15+01:00Saad JbabdiSignal either SMT or along orientationAt the moment all the red lines are SMT (except the plot against bvecs_z).
This ticket is about allowing user to choose whether they want the SMT or the signal along a given direction.
The proposal is to add a button that is by defau...At the moment all the red lines are SMT (except the plot against bvecs_z).
This ticket is about allowing user to choose whether they want the SMT or the signal along a given direction.
The proposal is to add a button that is by default ticked (SMT), and if it is not, the user can move sliders for theta/phi defining the single bvec.
@ndcn0236 what do you think of this feature?Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/103New preset for AxCaliber acq2021-08-02T12:37:04+01:00Saad JbabdiNew preset for AxCaliber acqAdd new preset for AxCaliber-style experiments (varying diffusion times)
- Get the parameters from [https://pubmed.ncbi.nlm.nih.gov/18506799/](https://pubmed.ncbi.nlm.nih.gov/18506799)Add new preset for AxCaliber-style experiments (varying diffusion times)
- Get the parameters from [https://pubmed.ncbi.nlm.nih.gov/18506799/](https://pubmed.ncbi.nlm.nih.gov/18506799)Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/100Download diffTime etc if available2021-08-02T12:37:23+01:00Saad JbabdiDownload diffTime etc if availableThe download scatter button currently only saves bvals/bvecs alongside scatter. Needs to save difftime etc if available.The download scatter button currently only saves bvals/bvecs alongside scatter. Needs to save difftime etc if available.Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/97Add log scale option for plots2021-08-02T12:37:13+01:00Sean FitzgibbonAdd log scale option for plotsI am thinking of adding new drop down buttons which interact with some of the x and axes. For example for plotting log of signal instead of signal, or plotting 1/sqrt(b) instead of b.I am thinking of adding new drop down buttons which interact with some of the x and axes. For example for plotting log of signal instead of signal, or plotting 1/sqrt(b) instead of b.Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/96Catch errors and present them to user2022-03-15T10:55:03+00:00Sean FitzgibbonCatch errors and present them to userPresent errors to the user in a sensible UI element rather than in the terminal.Present errors to the user in a sensible UI element rather than in the terminal.https://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/95Fix cylinder compartment2021-07-29T10:56:37+01:00Saad JbabdiFix cylinder compartmentCylinder and stick don't give the same signal when radius = 0
This was fixed by changing the way the bval is calculated. A test was added to ensure cyl(radius=0) == stickCylinder and stick don't give the same signal when radius = 0
This was fixed by changing the way the bval is calculated. A test was added to ensure cyl(radius=0) == stickSaad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/93Load acq other than bvals2021-08-04T18:23:48+01:00Saad JbabdiLoad acq other than bvalsAdd new loaders (or modify loader panel) to allow user to specify diffusion times, pulse durations, and gradient strengthAdd new loaders (or modify loader panel) to allow user to specify diffusion times, pulse durations, and gradient strengthHossein RafipoorHossein Rafipoorhttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/92New save data button2021-07-28T17:56:27+01:00Saad JbabdiNew save data buttonAdd button to save data (nifti?text?)
- Add a `Button` object near the new `Toggle` for showing data.
- Add a new function that returns a numpy array for the data.
- Button.on_click() will then allow user to select a file for saving the...Add button to save data (nifti?text?)
- Add a `Button` object near the new `Toggle` for showing data.
- Add a new function that returns a numpy array for the data.
- Button.on_click() will then allow user to select a file for saving the data. Possibly allow multiple file types for saving (e.g. numpy or ascii)Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/91Default not show data2021-07-28T14:26:15+01:00Saad JbabdiDefault not show dataModify the default display to not showing data (may require a toggle for showing data)
My plan is to add a `Toggle` button that is unticked by default. When ticked, the scatter points are shown.
To do so I will add a bokeh `Toggle` o...Modify the default display to not showing data (may require a toggle for showing data)
My plan is to add a `Toggle` button that is unticked by default. When ticked, the scatter points are shown.
To do so I will add a bokeh `Toggle` object to the `Acquisition` class. Then I'll add an if statement in the plotting functions to check if the button if checked before plotting.Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/89Fix Dispersion2021-08-02T14:57:55+01:00Saad JbabdiFix DispersionThe dispersion slider doesn't do anything at the moment and needs fixing.The dispersion slider doesn't do anything at the moment and needs fixing.Hossein RafipoorHossein Rafipoorhttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/88New plot: change vectors illustrating FA/MD dependence on parameters2021-06-09T17:26:45+01:00Michiel Cottaarmichiel.cottaar@ndcn.ox.ac.ukNew plot: change vectors illustrating FA/MD dependence on parametersCreates a new plot, which illustrates how a 10% increase in a microstructural parameter (e.g., from individual compartments) or acquisition parameters (e.g., b-value, diffusion time). As baseline would be taken the user-selected model pa...Creates a new plot, which illustrates how a 10% increase in a microstructural parameter (e.g., from individual compartments) or acquisition parameters (e.g., b-value, diffusion time). As baseline would be taken the user-selected model parameters and single-shell acquisition parameters. The central point corresponds to the FA/MD value for this set of parameters. This center would be marked for by a crosshairs to make it easier to see whether FA/MD increaseses/decreases.
Questions:
1. Should this include ODF parameters?
2. Should we just omit parameters we are not sensitive to (e.g., diffusion time for only Gaussian compartments, fibre orientation in case that they affect all parameters)?https://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/87User documentation / video tutorials2021-09-04T14:31:34+01:00Nicole EichertUser documentation / video tutorials# Improving documentation
There are two bits of documentation: the README on the main Git repo, and the Wiki page.
- README: currently ok, just need to make sure that the instructions are up to date, mention the contributors, and add ...# Improving documentation
There are two bits of documentation: the README on the main Git repo, and the Wiki page.
- README: currently ok, just need to make sure that the instructions are up to date, mention the contributors, and add maybe instructions for how to create a miniconda environment?
- Wiki: This could have some more informations on the tool. For example a description of the different panels in the app, a link to the main paper (from Danny's group) which describes all the models, and links to the video tutorials.
# Tutorial videos
We need a few videos that describe the functionalities and how to create different models and interact with them and understand the different plots. Bearing in mind that the interface might change in terms of its look after the videos have been made.
A list of possible videos:
- Introduction: global overview of the different panels and sliders. Perhaps using the Tensor model.
- Begin with the top panel (choose model)
- Explain different plots
- show how moving sliders change plots
- explain microstructure plots
- move on to the acquisition panel and display HCP data
- add noise
- save data
- show saved file
- the end
- Ball and Stick
- Here create ball+stick
- explain behaviour of each panel
- explain FOD panel
- add crossings / dispersion
- interact with glyph using acq param changing panel
- NODDI
- csf+zeppelin+stick
- dispersion applied to both stick and zeppelin
- examine the different figures
- SANDI
- sphere+zeppelin+stick+dispersion
- opportunity to talk about diffusion time dependence
- examine different figures
- look at cylinder (ax-caliber model)Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/86Come up with new plots2021-07-22T11:58:31+01:00Nicole EichertCome up with new plotshttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/84Disable point plots button2021-07-11T14:50:57+01:00Nicole EichertDisable point plots buttonhttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/83Fix bvals/bvecs selector2021-06-07T12:32:36+01:00Saad JbabdiFix bvals/bvecs selectorThe bvals/bvecs selector is broken and needs fixing.The bvals/bvecs selector is broken and needs fixing.Saad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/81Fix cylinder2021-05-28T13:55:35+01:00Saad JbabdiFix cylinderSaad JbabdiSaad Jbabdihttps://git.fmrib.ox.ac.uk/fsl/DIVE/-/issues/80update Readme2021-06-07T12:29:55+01:00Nicole Eichertupdate ReadmeNicole EichertNicole Eichert