This is version 2.2 of the AFNI FATCAT (Functional And Tractographic Connectivity Analysis Toolbox) demo set (Taylor & Saad, 2013, in Brain Connectivity). * In updating from v2.1 -> v2.2, the scripts around the ROI selection for post-FreeSurfer/connectomic tracking have changed. There have also been a few naming changes, reflecting some changes in AFNI program functionality. * This demo set consists of DWI and RS-FMRI data, as well as example HARDI-reconstructions, some of which has been processed using AFNI, FSL (such melodic for ICA), dcm2nii and DSI-Studio (for HARDI-modeling) programs. The FATCAT programs run from commandlines. Here, short examples and scripts of several, but not all, programs and features are given in the Do_* files. The primary purpose of these scripts is to provide a number of realistic and/or didactic examples for using FATCAT programs in MRI analysis. Thus, there are descriptions, musings and suggestions in the comments in each Do_* file. There are roughly three sets of analyses, which are not really independent. There is one for DTI, one for HARDI and one for RSFC. Particularly for DTI and HARDI outputs, there are a number of script examples for viewing results nicely in SUMA, courtesy of ZS Saad. Users are encouraged to check the outputs of each program, even when scripts are not given. Work is currently being done for a tutorial using the SUMA-visualization tools, though some scripts are provided here for viewing features. Additionally, work will continue on the HARDI features, for example for including a more rigorous method for treating directional uncertainty. *********************************************************************** To run a script, one should simply be able to type, for example, the followin in a commandline: $ tcsh Do_01_RUNdti_convert_grads.tcsh or $ ./Do_01_RUNdti_convert_grads.tcsh and similarly for each Do_* file. Some of these scripts use existing AFNI programs, such as 3dDWItoDT and 3dcalc, as well. They should generally be run in the order of enumeration (first Do_01*, then Do_02*, etc.) since outputs from some steps become inputs for others. If you want a shortcut to run all calculations-scripts, but not the visualization ones, then run Do_00_PRESTO*.tcsh. Even so, it's worth reading through some of the comments and descriptions in the comments of each file. Questions/comments/suggestions are always welcome, either on the AFNI Message Board website, or via email: PA Taylor: neon.taylor@gmail.com ZS Saad: saadz@mail.nih.gov *********************************************************************** + SCRIPTS to run (more detailed description in comments of each): Do_00_PRESTO_ALL_RUNS.tcsh :Execute all Do_*RUN*.tcsh scripts Do_01_RUNdti_convert_grads.tcsh :turn outputs from dcm2nii into usable gradient columns, includes component flipping and b0 removal Do_01_RUNhardi_convert_grads.tcsh :turn outputs from dcm2nii into usable b-table columns for DSI-Studio Do_02_RUNdti_DW_to_DTI.tcsh :calculate tensor and associate parameters from DWIs (stored in directory called DTI). Do_03_RUNdti_make_network_ROIs.tcsh :estimate ROIs for tractography from RS- FMRI data contained in SOME*, which contains some ICA output components (NB: file SOME* has been mapped into native DW space). Do_04_RUNdti_match_network_ROIs.tcsh :match IC Z-score maps of individual's data with a reference set Do_05_RUNdti_DET_tracking.tcsh :deterministic tractography examples for DTI model data, highlighting various options and user-control features Do_05_RUNhardi_DET_tracking.tcsh :deterministic tractography examples for HARDI model data, highlighting various options and user-control features Do_06_VISdti_SUMA_visual.tcsh :fun SUMA visualization of tract output, as well as WM-ROI statistics, all in one. Do_07_RUNdti_uncertainty_est.tcsh :in preparation for both mini- and full- probabilistic tracking, here we calculate uncertainty estimates of some DT parameters. Do_07_RUNhardi_uncertainty_est.tcsh :since the HARDI modeling is not currently performed in AFNI/FATCAT, there isn't a program for calculating uncertainty of parameters, such as there is for DTI using 3dDWUncert. This describes a *very* simplistic method for assigning approx. values of uncertainty for parameters. Do_08_RUNdti_miniprob_track.tcsh :simple extension of deterministic tracking to include some tensor perturbations + Monte Carlo iterations; output is essentially the same style as for purely deterministic, but gives a broader picture of potential tract estimations including tensor uncertainty Do_08_RUNhardi_miniprob_track.tcsh :simple extension of deterministic tracking (as above) for HARDI case Do_09_VIS*tcsh :more visualization & comparison Do_10_RUNdti_fullprob_track.tcsh :run probabilistic tractography for DTI data Do_10_RUNhardi_fullprob_track.tcsh :run probabilistic tractography for HARDI data Do_11_VIS*tcsh :more visualization of probabilistic output Do_12_RUNrsfc_netw_corr.tcsh :calculate correlation matrices of functional ROI networks, particularly for accompanying some of the statistical WM- ROI output obtained from tractography Do_13_RUNrsfc_RSFCfilt_param.tcsh :final step of processing for resting state time series, bandpassing to low frequency fluctuations (LFFs); at this step, several spectral coefficients can be calculated such as ALFF, fALFF, etc. Do_14_RUNrsfc_ReHo_param.tcsh :calculate Kendall's W (coefficient of concordance, or ReHo=Regional Homogeneity) for functional LFFs output by RSFCfilt *********************************************************************** Briefly, the data files contained in this demo are: + DWI data from scanning: AVEB0_DWI.nii.gz mask_DWI+orig.* bval bvec + RS-FMRI from scanning, processing, and also ICA (NB: mapped into DWI space): REST_in_DWI.nii.gz SOME_ICA_NETS_in_DWI+orig.* + ANATOMICAL data and skull-stripped surface: mprage+orig.* toy.gii + PARAMETER files for running deterministic and probabilistic tractography (with some important differences in formats between the *.niml.opts and *dat): ALGOPTS_DET.niml.opts ALGOPTS_PROB.dat + MNI reference IC bricks mapped into DWI for reference: MULTISITE_in_DWI+orig* + HARDI-modeled data (from the same AVEB0_DWI.nii.gz) from DSI-Studio, using GQI reconstruction; also included is the example script of DSI-Studio commands used for constructing and converting the data to NIFTI files: HARDI/GQI*.nii.gz HARDI/do_dsistudio.tcsh