# **GIFT Updates**
## GIFT 4.0.5.0 (Feb 20, 2024):
- Changed name of Neuromark template to Neuromark_fMRI_1.0.nii
- Added Neuromark fMRI 2.0
- Multiorder constrained maps supplied
- Implemented Datavis
- GIFT version displayed in main window
- Added automatic slicing feature for both fMRI and SBM
- Implemented single side band modulation sliding window Pearson correlation (SSB+SWPC) option by Dr. Ashkan Faghiri
- Default&ICV mask option to remove eyeballs
- Implemented NBIC toolbox, including import function and example script
- GIFT MATLAB Runtime Compiler
- Reports working
- Removed rspm_progress_bar in deployed cases (preventing a crash)
- Modified report for bidsapp
- MANCOVAN
- F-stat option when using univariate results (icatb_defaults)
- contrasts label excludes nan in univariate results
- ANOVA fixes
- New demo data for GIFT (Stefan Dvoretski )
- Fixed report generation for spatial constraint ica
- Fix of "out of range" error when inconsistency between comp_network_names, sesInfo.numComp and number of subjects appears
- Batch fix for head motion variables
- GIFT will pick the batch file TR for DFNC processing if if TR is different in the parameter file
- Corrected icasso figures plots out as they should when clicking button [Results Summary]
- T-test added to SBM
- ROI based FC stats summary is now saved
- Plotting components faster
- Trilinear interpolation for the display of function on the structural template (icatb_default.m)
- Implemented cEBM to GIFT
- Added colorbar to icatb_overlayImages
- For batch fix so folder is created even if extra slash is supplied
- Fix for matlab2023b bug
- Default&icv mask for GIFT when run on server installation
- Added average mask for fMRI
- Fixed report generation for Windows platform
- ROI-voxel option in dFC tool fixed so voxel maps are not prevented
- groupica.m now handles multiple arguments when called in batch
***
## Miscellaneous enhancements & fixes to GroupICAT v4.0c (Feb 24, 2022):
- Using double precision to avoid any errors in the spatial chronnectome when using default despike option
- Display results structure is added in nipype model file, including network summary options
- Gig-ica algorithm name is changed to MOO-ICAR
- Subject ICA loadings are generated when using algorithms like Infomax, fast ICA, etc
- Default template is changed to ch2bet_3x3x3mm.nii
- Evaluation criteria for estimating clusters like daviesbouldin and ray turi
- icatb_nan_mT function handles multiple contrasts
- Kurtosis graphs y limits are changed separately for the spatial maps and timecourses
- Subject loading coefficients are written
- Updated mex binaries, including for SPM12
- Option added, to remove components from testing data-sets in the noise cloud toolbox
- Timecourses entered as row vectors are internally converted to column vectors
- Merge analysis only uses timecourse information if spatial components information is not present
- Added INTERP_VAL interpolation when resizing images (icatb_defaults.m)
- GIFT now creates output directory when saving concatenated component timecourses
- Nans are used in timecourses or fnc correlations if subject back-reconstucted files are missing
- Added modified getStateCorrs sub-function (originally found in icatb_post_process_dfnc.m) to roi-based dFC post-processing. Adds call to getStateCorrrs after kmeans clustering is run on the full input dataset (all subjects and windows). This provides users with two additional fields (corrs_state and states) in clusterInfo which are needed for group or individual subject analyses.
- Added options to turn off mutual information and kurtosis in reports
- MOO-ICAR option is changed to use reference file names instead of reference data to handle large number of references
- icatb_save ica data is handled to use single component
- Post process timecourses is saved incrementally
- Added options to compute aggregate spectra, fnc, etc in post process step to speedup display results. Files are saved individual subject-wise instead of one big file.
- Options are provided to compute aggregate fnc, spectra, etc in post-process step. Individual subject files are saved instead of one big file.
- "chkSize undefined value", "too many input args", "Brace indexing is not supported for this variable type", missing field "postprocess" and "Error using reshape" errors fixed
- Anisotropic template is resliced to isotropic
- Tall array DFNC option added when using kmeans
- Ratio to interpolate is computed once and used in resampling timecourses when the TRs are different across subjects
- r_to_z function is used instead of atanh
- Added IVA-L-SOS-Adaptive algorithm
- iva second order is updated to use only weight change as the stopping criteria
- Options to initialize weights using IVA-G
- Colormap is used in figure property instead of calling colormap function
- Option to store FNC matrices displayed in field wfcInfo.display_info.FNC
- Option to replace gig-ica with MOO-ICAR to read batch file inputs from previous version
- Options to initial centroids as user input in standard dfnc
- Supporting coregistering files when the format is nifti gzip
- Report generator allows results structure in mat file and is opened in background mode when using GUI to handle empty plots
- options are added in defaults to write stats info (mancova) and spectra.
- Spm stats, calculate stats and single trial amplitude are removed from options dropdown box
- Warning message related to eigs function is fixed
- Decentralized option in mancova
- Option is provided to use spectra options like Npoint FFT and bins when TIMECOURSE_POSTPROCESS.spectra.option is set to 2
- Added decentralized mancova options
- Input Kmeans centroids are back-projected on to the data to find centroids on the new data-set
- Power spectra is computed using pwelch
- Fixed gii file issue which gives error no private field
- Added algorithm table
- Use gray instead of white color for separating cells in the matrix plot
- FNC network plot is used when network names are passed in the univariate results
***
## GroupICAT v4.0c (Oct 10, 2020):
- We upgraded some tools like adding neuromark template in constrained ica, display summary tools for source based morphometry and mancovan toolbox in the stand alone version of gift. Docker for group ica is now available. Please download tools at https://trendscenter.org/software/gift/. Docker can also be accessed using https://github.com/trendscenter/gift-bids.
- New GUI is provided to run automated ICA algorithms like MOO-ICAR (previously GIG-ICA) and Constrained ICA (spatial) with less options. This option can be accessed when you click on Setup ICA analysis button. Batch example is given in icatb/icatb_batch_files/batch_constrained_ica.m.
- Option is now provided to use an average mask in setup ICA analysis. Mask option can be accessed in “Setup-ICA defaults” menu.
- Some more dimensionality estimation options are provided in the Setup ICA analysis like:
- MDL (FWHM): This option skips i.i.d sampling. You need to enter smoothness FWHM kernel used on the fMRI data.
- Order estimated by entropy rate based methods (finite memory length and AR signal).
- Some more despike options are provided like despike based on smoothed timecourses as reference signal and median filtering. You can change these options in variable DESPIKE_OPTIONS in icatb_defaults.m.
- Batch option to do univariate tests directly is provided in the Mancovan toolbox. Options are provided to handle missing subjects at a particular voxel, frequency bin or FNC component pairs. Example templates are given in icatb/icatb_batch_files/input_mancovan_ttests.m.
- Option is now provided to use GIFTI data as input in SBM toolbox.
- Options are provided to merge separate ICA analyses in the Mancovan or dFNC along the subject dimension or component dimension (model order analysis given the same subjects). For more information, please see icatb/icatb_batch_files/inp
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miniz.c 380KB
nifti_stats.c 290KB
shoot_regularisers.c 52KB
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spm_krutil.c 15KB
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spm_mrf.c 12KB
shoot_optim3d.c 11KB
shoot_multiscale.c 10KB
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spm_bwlabel.c 9KB
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mat2file.c 9KB
jsmn.c 9KB
spm_render_vol.c 8KB
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spm_field.c 8KB
spm_mesh_utils.c 7KB
spm_unvec.c 7KB
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spm_bsplins.c 6KB
spm_hist2.c 6KB
icatb_eig_symm_sel.c 6KB
spm_dilate_erode.c 5KB
spm_matfuns.c 5KB
spm_bsplinc.c 5KB
shoot_expm3.c 5KB
init.c 5KB
icatb_eig_symm_all.c 5KB
spm_project.c 5KB
spm_resels_vol.c 4KB
nifti_stats_mex.c 4KB
spm_gamrnd.c 3KB
spm_sample_vol.c 2KB
zstream.c 2KB
spm_global.c 2KB
spm_slice_vol.c 2KB
spm_getdata.c 1KB
spm_existfile.c 1KB
spm_unlink.c 1001B
shoot_boundary.c 897B
spm_hist.c 784B
ImageSelection.class 1KB
contents 9B
findjointstateab.cpp 7KB
estpab.cpp 6KB
estpa.cpp 5KB
spm_mesh_reduce.cpp 4KB
estmutualinfo.cpp 3KB
estcondentropy.cpp 2KB
estjointentropy.cpp 1KB
estentropy.cpp 1KB
style.css 1KB
aod_regressors.dat 110KB
visuomotor_regressors.dat 11KB
glmnetMex.dll 144KB
estpa.dll 40KB
findjointstateab.dll 40KB
estcondentropy.dll 40KB
estentropy.dll 40KB
estjointentropy.dll 40KB
estmutualinfo.dll 40KB
estpab.dll 40KB
icatb_eig_symm_sel.dll 8KB
icatb_eig_symm_all.dll 7KB
v4.0b_gica_manual_jan16_2020.docx 4.48MB
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glasso.F 19KB
glmnetMex.F 11KB
glmnetMex.matlabR13.F 10KB
noisecloud_gui.fig 230KB
setup_dyn_fc.fig 191KB
dfnc_toolbox.fig 112KB
mancovan_toolbox.fig 88KB
dyn_fc_toolbox.fig 77KB
spatial_chronnectome.fig 74KB
post_process_spatial_chronnectome.fig 44KB
gift.fig 32KB
sbm.fig 32KB
post_process_dfnc.fig 30KB
setup_reference_ica.fig 28KB
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