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NeuroElf feature requests


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:

  • check whether (and if so since when) the feature/format you wish to request is already on the list below
  • write an email to info (AT) neuroelf (DOT) net, stating the request (or asking to prioritize the request)
  • wait for a reply by email and also…
  • check back on this page to see if it's on the list or the status has been updated

Feature requests

I have decided to create separate lists for

  • features of use which seem either relatively easy to implement (short time) or of high interest (important additions for the toolbox)
  • features that seem useful but might take very long to implement or where the use is limited to a very specific application
  • features which I consider not suitable or of too little use for the toolbox (in which case I would also give a short comment as to why I believe so)
  • features that were requested and which have been implemented

To be implemented

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

Potential candidates

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

Unlikely candidates

Feature name Requested by Request date Description Reason for exclusion from list of likely candidates

Already implemented

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
neuroelf_feature_requests.txt · Last modified: 2011/05/08 04:19 by jochen