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neuroelf_feature_requests [2010/06/19 22:25]
jochen added multiple kernels for flexinterpn
neuroelf_feature_requests [2011/05/08 04:19] (current)
jochen moved two features to implemented section
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 //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...// //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...//
 +
 +===== Procedure =====
 +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 ===== ===== Feature requests =====
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 ==== To be implemented ==== ==== To be implemented ====
 ^ Feature name              ^ Requested by       ^ Request date  ^ Description ​ ^ Status ​ ^ ^ 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 ​ | | 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 ​ |
-| combining VMPs (in GUI)   | Hedy Kober         | 5/​18/​2010 ​    | dialog that allows to flexibly combine maps from several VMP containers, if necessary with resampling/​relocation of data  | in pipeline ​ | 
-| 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! ​ | 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 ​ | | 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 ​ | | 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 ​ |
-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 completeit would of course be nicer for that feature to work!  | in pipeline ​ | +weighted data             | Jochen Weber       ​| ​4/12/2011     | start with data acquisitionweights = 1, then, during each processing/analysis stepcarry over weights ​as estimate of plausibility of datause weights for all subsequent steps  ​| ​not sure yet  | 
-| 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 ​ | +VTC/VOI-network analysis ​ | Jochen Weber       ​| ​4/12/2011     | different options ​to assess suspected network nodes of VOIs (correlation matrices, differences ​in correlations across conditionsGranger, SEM?, robust option, etc.)  | not sure yet  | 
-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) ​ | in pipeline ​ | +
-| SDM::​CalcBetas update/​fix ​ | Jochen Weber      | 5/​20/​2010 ​    | after code inspectionI realized that some features only exist in the help (masking/​thresholding/​global signal as nuisance); adding that code!! ​ ​| ​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 ​ | +
-| 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  | in pipeline ​ |+
  
 ==== Potential candidates ==== ==== Potential candidates ====
 ^ Feature name              ^ Requested by       ^ Request date  ^ Description ​ ^ Comment ​ ^ ^ 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 ​ | | 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 ​ |
-| 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 ​ | probably doable in a few days of coding, very likely ​ | 
 | 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 ​ | | 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 ​ |
  
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 ==== Already implemented ==== ==== Already implemented ====
 ^ Feature name              ^ Requested by       ^ Request date  ^ Description ​ ^ Implemented in version ​ ^ ^ 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 ​ | v0.9a SNAPSHOT ​ | +| 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) ​ | v0.9a SNAPSHOT ​ | +| 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  | v0.9a SNAPSHOT ​ | +| 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  | v0.9a SNAPSHOT ​ | +| 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 ​ | v0.9a SNAPSHOT ​ | +| 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) ​ | v0.9a SNAPSHOT ​ | +| 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! ​ | v0.9a SNAPSHOT ​ | +| 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 ​ | v0.9a SNAPSHOT ​ | +| 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)  | v0.9a SNAPSHOT ​ |+| 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 ​ | | 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.1276979145.txt.gz · Last modified: 2010/06/19 22:25 by jochen