Many (if not most) of the features being implemented in NeuroElf have been requested by colleagues. While I enjoy the process of developing algorithms and translating them into Matlab, I usually require that the product of my work is actually used. Hence I would say that if you think a feature you are missing could be of use for several labs/researchers, you are welcome to submit it for inclusion into this list (which I will update whenever a feature becomes requested or available).
Comment: the fact that most features on the list were requested on May 18th 2010 is because I presented the toolbox to the SCN lab meeting that day…
In case you have a feature (or file format) request, please follow these steps:
I have decided to create separate lists for
| Feature name | Requested by | Request date | Description | Status |
|---|---|---|---|---|
| HDR menu → segmentation | Jochen Weber | 4/12/2011 | adding segmentation (SPM-based) to the HDR menu | in pipeline |
| ComputeFormula also for SMP | Jochen Weber | 4/12/2011 | add support for SMP::ComputeFormula (either different or combined implementation | in pipeline |
| physio confounds | Lauren Atlas | 4/18/2011 | support to automatically create confound regressors from physio (ECG) data, still needs specs! | in pipeline |
| better subject-specific VOI support | Hakwan Lau | 4/18/2011 | support for subject specific VOIs in ne_mdmvoicondavg → MDM::VOITimeCourses, and throughout | in pipeline |
| VOI time course plot | Jochen Weber | 4/20/2011 | option to plot VOI time courses (probably from within ne_mdmvoicondavg dialog), incl. PRT information | in pipeline |
| multi-study (MDM) dialog enhancements | SCAN Unit | 4/20/2011 | add RunTimeVars.Discard inspection/update feature into dialog; also feature to see condition names from models, options for single-trial GLM and PPI | in pipeline |
| fmriqasheet enhancements/fix | SCAN Unit | 4/20/2011 | 1. percentage of outlier volumes is incorrect; 2. UI should get a dialog to assess multiple scans, give results for multiple scans, have options (e.g. realignment); 3. link fmriqasheet output to object.RunTimeVars.Discard field | in pipeline |
| SDM::CalcBetas | SCAN Unit | 4/20/2011 | make it optional to first project out confounds (filters, motion) of both data and remaining model and then perform regression (thorough testing after implementation!!) | in pipeline |
| SDM::CalcBetas check/fix | Jochen Weber | 5/20/2010 | after code inspection, I realized that some features only exist in the help (masking/thresholding/global signal as nuisance); adding that code!! | in pipeline |
| local storage of configs | Nick Ketz | 5/18/2010 | in a network-based software setup (central installation of NeuroElf), the configuration files are currently shared (as they live in the installation folder); either make the filenames local (e.g. based on username) or store locally (in user folder) | in pipeline |
| spm5_prepro enhancement | Jen Silvers | 6/8/2010 | option to set a filename pattern for the VTCs that are created after preprocessing | in pipeline |
| spm5_prepro improvements | Hedy Kober et al. | 5/18/2010 | more flexibility w.r.t. subject normalization (support for EPI template, DARTEL toolbox), text field for number of skipped volumes, setting origins/orientation of source data (fewer problems during normalization/coregistration), option to purge intermediate preprocessing steps (less storage on disk required) | in pipeline |
| importvmp dialog enhancement | Hedy Kober | 5/18/2010 | allowing the user to specify Analyze/NIftI files containing maps from several folders | in pipeline |
| normalization check | Jochen Weber | 5/18/2010 | automatic generation (update) of a multi-subject/multi-session VTC (or other format) to quickly verify (via eyeballing) that the normalization has worked alright | in pipeline |
| weighted data | Jochen Weber | 4/12/2011 | start with data acquisition, weights = 1, then, during each processing/analysis step, carry over weights as estimate of plausibility of data; use weights for all subsequent steps | not sure yet |
| VTC/VOI-network analysis | Jochen Weber | 4/12/2011 | different options to assess suspected network nodes of VOIs (correlation matrices, differences in correlations across conditions, Granger, SEM?, robust option, etc.) | not sure yet |
| Feature name | Requested by | Request date | Description | Comment |
|---|---|---|---|---|
| Granger causality | Jochen Weber et al | 5/18/2010 | computing of Granger causality, both in the BrainVoyager pair-wise style, but also in a network-like way (comparable to the toolbox of Anil Seth in Matlab) | needs a lot of research and coding effort, decision pending |
| improvement of PPI | Ajay Satpute at al | 5/18/2010 | the new PPI-like feature (MDM::ComputeGLM) should be improved (to allow the SPM-typical deconvolution and reconvolution) | will require quite some additional coding |
| Feature name | Requested by | Request date | Description | Reason for exclusion from list of likely candidates |
|---|
| Feature name | Requested by | Request date | Description | Implemented in version |
|---|---|---|---|---|
| GUI: define ROI feature | Jochen Weber | 5/18/2010 | the actual code to create a VOI from the marked voxels was missing | v0.9b |
| GUI: local maxima checkbox | Kevin Ochsner | 5/18/2010 | prior to the implementation, users needed to press the “L” key to disable/enable local maxima splitting of clusters (and the state of that flag was invisible) | v0.9b |
| GUI: goto nearest maximum | Kevin Ochsner | 5/18/2010 | the GUI should allow users to set the current position of the cursor to the closest voxel that was determined as a maximum of an earlier cluster table call | v0.9b |
| GUI: flexible contrast weights | Ajay Satpute | 5/18/2010 | allowing users to edit contrast weights by entering a number instead of the less flexible +1/-1/0 and subsequent balancing logic | v0.9b |
| ClearObjects (xff method) | Nick Ketz | 5/18/2010 | giving users an option to clear several objects at once that match a common filename pattern | v0.9b |
| any2ascii overload | Jochen Weber | 5/18/2010 | overloading of other classes (xfigure, xff) to allow passing of objects in ASCII format (e.g. for GUI elements) | v0.9b |
| tff optional as binary | Jochen Weber | 5/30/2010 | for large text-based files (FBR), there is a high speed-up potential if the file is read and parsed as binary content – implemented for testing! | v0.9b |
| masks from VMPs in GUI | Ethan Kross | 5/29/2010 | giving the user a simple option to convert the current statistical selection (height and size threshold of currently displayed map/s) into a BrainVoyager compatible MSK object | v0.9b |
| echo mode in GUI | Nick Ketz | 5/18/2010 | GUI should give the names of functions/methods called (to allow users to script their actions in a simple way) | v0.9b |
| GSR data processing | Rich Lopez | 5/19/2010 | processing of GSR data with automatic filtering and signal detection | v0.9b SNAPSHOT |
| flexinterpn multiple kernels | Jochen Weber | 6/19/2010 | option to pass multiple kernels (one per dimension) to flexinterpn, which then allows smoothing in one dimension only | v0.9b SNAPSHOT |
| plotcurves improvements | Jochen Weber | 6/19/2010 | adding type cue; making spots “fixed” (certain types, such as onset/cue); adding key-commands for “find max in window”, “find min in window” | v0.9b SNAPSHOT |
| GUI-based origin setting | Jochen Weber | 5/19/2010 | enhanced way to specify the origin and orientation of a dataset by allowing the user to drag (and shift+drag) the dataset for translation (and rotation) feature implemented differently | v0.9b SNAPSHOT |
| showspmrparams enhancement | Hedy Kober | 6/28/2010 | legend next to plots and keeping the colors the same as SPM | v0.9b SNAPSHOT |
| mediation | Jochen Weber et al | 5/18/2010 | support (or integration) of Tor Wager's mediation toolbox so as to have it work with all supported file formats implemented for the RFX-GLM format, currently only single-level mediation | v0.9b SNAPSHOT |
| add GUI code for MDM::ComputeGLM | Hedy Kober | 5/18/2010 | add the code for the GUI dialog to locate VTC/SDM/PRT/RP files for MDM::ComputeGLM | v0.9b SNAPSHOT |
| GLM::VOITimeCourses | Jochen Weber | 6/30/2010 | ability to extract timecourses from referenced VTCs in a GLM | v0.9b SNAPSHOT |
| combining VMPs (in GUI) | Hedy Kober | 5/18/2010 | dialog that allows to flexibly combine maps from several VMP containers | v0.9b SNAPSHOT |
| importrfxglm bug fix | Jochen Weber | 5/18/2010 | currently the condition selection in importrfxglmfromspms does not allow to specify the conditions to be imported; while they can be easily removed after the import is complete, it would of course be nicer for that feature to work! | v0.9c |
| CreateSMP from VMP to AFT | Jochen Weber | 4/12/2011 | change the code so that it works for all map type objects (incl. CMP, GLM, HEAD, HDR, VMP) | v0.9c |
| NII export support for GLM/VMP formats | Hakwan Lau | 4/18/2011 | so far, the output method is limited to HDR/IMG, also support NII (checking that exported files contain valid transformation matrix!) | v0.9c |
| mutliple scatters | Jen Silvers | 5/18/2010 | ability to plot several, independent scatter plots in the GUI (e.g. for multiple groups of subjects or to compare conditions; interface still requires specification! probably define separate scatter types/colors per group with default being using the same; if split perform regression per group | v0.9c |
| legend on bar plot | SCAN Unit | 4/20/2011 | add optional legend to bar plot | v0.9c SNAPSHOT |
| full support for 3D/4D HDR/NII MAT files | Jochen Weber | 4/12/2011 | support for SPM's 4D (and older 3D) MAT files with (different) quaternion matrices for each volume (sampling, updating, etc.) | v0.9c SNAPSHOT |