fcMRI preprocessing including nuisance variable regression
Attention!
fcMRI_preproc_161012 assumes successful completion of BOLD preprocessing (:ref:`cross_bold_pp_161012`).
Usage: fcMRI_preproc_<version>.csh <params file> [instructions file]
Examples:
fcMRI_preproc_161012.csh VB16168.params
Required parameters
| Variable | Values | Description |
|---|---|---|
| patid | |patid_vals| | |patid_desc| |
| target | |target_vals| | |target_desc| |
| FSdir | |FSdir_vals| | |FSdir_desc| |
| srcdir | |srcdir_vals| | |srcdir_desc| |
| fcbolds | |fcbolds_vals| | |fcbolds_desc| |
| TR_vol | |TR_vol_vals| | |TR_vol_desc| |
| CSF_lcube | |CSF_lcube_vals| | |CSF_lcube_desc| |
| CSF_sd1t | |CSF_sd1t_vals| | |CSF_sd1t_desc| |
| CSF_svdt | |CSF_svdt_vals| | |CSF_svdt_desc| |
| WM_lcube | |WM_lcube_vals| | |WM_lcube_desc| |
| WM_svdt | |WM_svdt_vals| | |WM_svdt_desc| |
Optional parameters
| Variable | Values | Default | Description |
|---|---|---|---|
| FCdir | |FCdir_vals| | |FCdir_default| | |FCdir_desc| |
| day1_patid | |day1_patid_vals| | |day1_patid_desc| | |
| MB | |MB_skip_vals| | |MB_skip_default| | |MB_skip_desc| |
| blur | |blur_vals| | |blur_default| | |blur_desc| |
| bpss_params | |bpss_params_vals| | |bpss_params_desc| | |
| conc | |conc_vals| | |conc_desc| | |
| fmtfile | |fmtfile_vals| | |fmtfile_desc| | |
| FDthresh | |FDthresh_vals| | |FDthresh_desc| | |
| FDtype | |FDtype_vals| | |FDType_default| | |FDtype_desc| |
| anat_aveb | |anat_aveb_vals| | |anat_aveb_default| | |anat_aveb_desc| |
| anat_avet | |anat_avet_vals| | |anat_avet_default| | |anat_avet_desc| |
| min_frames | |min_frames_vals| | |min_frames_fcpreproc_default| | |min_frames_desc| |
| CSF_excl_lim | |CSF_excl_lim_vals| | |CSF_excl_lim_default| | |CSF_excl_lim_desc| |
| task_regressor | |task_regressor_vals| | |task_regressor_desc| | |
| noGSR | |noGSR_vals| | |noGSR_default| | |noGSR_desc| |
Processing steps
| Step description | Function | Output |
|---|---|---|
| Generate FS masks if they don't already exist | :ref:`Generate_FS_Masks_AZS` | atlas/ |br| <patid>_orig_to_<target>_t4 |br| <patid>_FSWB_on_<target>_333.4dfp.img |br| <patid>_GM_on_<target>_333_comp_b60.4dfp.img |br| <patid>_(WM,CS)_erode_on_<target>_333_clus.4dfp.img |
| Create conc file | :ref:`conc_4dfp` | <FCdir>/ |br| $conc |br| or, <patid>[_faln_dbnd]_xr3d_uwrp_atl.conc |
| Compute frame censoring using FD (if $FDthresh specified) and DVARS -- skipped if $fmtfile is specified | FD.awk, :ref:`run_dvar_4dfp` | movement/ |br| <patid>[_faln_dbnd]_xr3d.FD |br| atlas/ |br| <patid>[_faln_dbnd]_xr3d.FD.format (if $FDthresh) |br| <patid>_func_vols(.vals, .dat, .crit, .xmgr, .format) |
| Create average censored image | :ref:`actmapf_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_ave.4dfp.img |
| Compute defined mask and apply it | :ref:`compute_defined_4dfp`, :ref:`maskimg_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_dfnd.4dfp.img |br| atlas/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_dfndm.4dfp.img |
| Compute initial sd1 mean | :ref:`var_4dfp`, :ref:`qnt_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_sd1.4dfp.img |
| Make timeseries zero mean | :ref:`var_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_uout.conc |
| Make movement regressors for each bold run | :ref:`mat2dat`, :ref:`conc_4dfp`, :ref:`bandpass_4dfp`, :ref:`4dfptoascii` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_dat.conc |br| <patid>[_faln_dbnd]_xr3d_dat_bpss.conc |br| <patid>_<patid>_mov_regressors.dat |
| Temporal bandpass filter using $bpss_params | :ref:`bandpass_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss.conc |
| Make whole brain regressors including the 1st derivative | :ref:`qnt_4dfp` | <FCdir>/ |br| <patid>_WB_regressors_dt.dat |
| Make extra-axial CSF regressors (thresholded at $CSF_excl_lim) | :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` | <FCdir>/ |br| <patid>_CSF_mask.4dfp.img |br| <patid>_CSF_dies.4dfp.img |br| <patid>_CSF_regressors.dat |
| Make venticle regressors | :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` | <FCdir>/ |br| <patid>_vent_mask.4dfp.img |br| <patid>_vent_dies.4dfp.img |br| <patid>_vent_regressors.dat |
| Make white matter regressors | :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` | <FCdir>/ |br| <patid>_WM_mask.4dfp.img |br| <patid>_WM_dies.4dfp.img |br| <patid>_WM_regressors.dat |
| Paste nuisance regressors (mov, CSF, vent, WM, task) together and run covariance analysis | :ref:`covariance` (-D250) | |
| Paste together WB and WB derivative, and covaried nuissance regressors | <FCdir>/ |br| <patid>_nuisance_regressors.dat | |
| Remove nuisance regressors out of volumetric time series | :ref:`glm_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid.conc |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_coeff.4dfp.img |
| Compute sd1 mean for bandpass-filtered and nuisance regressed data | :ref:`var_4dfp`, :ref:`qnt_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_sd1.4dfp.img |br| (comparison to initial WB mean reported to stdout) |
| Spatial blur with f_half = $blur if specified | :ref:`gauss_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g<blur>.conc |
| Compute sd1 mean for blurred data if $blur | :ref:`var_4dfp`, :ref:`qnt_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g<blur>_sd1.4dfp.img |br| (mean reported to stdout) |
compute multi-volume correlation maps
Attention!
seed_correl_161012 assumes successful completion of BOLD preprocessing (:ref:`cross_bold_pp_161012`) and fcMRI preprocessing (:ref:`fcMRI_preproc_161012`).
Usage: seed_correl_161012.csh <parameters file> [instructions] [options]
Examples:
seed_correl_161012.csh VB16168.params
Options
| -noblur | analyze unblurred version of preprocessed data |
| -A | use format in atlas subdirectory (default FCmaps directory) |
Required variables
| Variable | Values | Description |
|---|---|---|
| patid | |patid_vals| | |patid_desc| |
| ROIdir | |ROIdir_vals| | |ROIdir_desc| |
| skip | |skip_vals| | |skip_desc| |
ROI specification variables (required)
| Variable | Values | Description |
|---|---|---|
| Option 1 | ||
| ROIimg | |ROIimg_vals| | |ROIimg_desc| |
| Option 2 | ||
| ROIlist | |ROIlist_vals| | |ROIlist_desc| |
| Option 3 | ||
| ROIlistfile | |ROIlistfile_vals| | |ROIlistfile_desc| |
Optional variables
| Variable | Values | Default | Description |
|---|---|---|---|
| FCdir | |FCdir_vals| | |FCdir_default| | |FCdir_desc| |
| MB | |MB_skip_vals| | |MB_skip_default| | |MB_skip_desc| |
| blur | |blur_vals| | |blur_default| | |blur_desc| |
| bpss_params | |bpss_params_vals| | |bpss_params_desc| | |
| conc | |conc_vals| | |conc_desc| | |
| fmtfile | |fmtfile_vals| | |fmtfile_desc| |
Processing Steps
| Step description | Function | Output |
|---|---|---|
| Create (multi-volume) ROI image if $ROIlistfile or $ROIlist specified | :ref:`paste_4dfp` | |
| Calculate seed (ROI) regressors | :ref:`qntm_4dfp` | <FCdir>/ |br| <patid>_seed_regressors.dat |br| <patid>_seed_regressors.rec |
| Compute total correlations | :ref:`glm_4dfp` (-t) | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr.4dfp.img |
| Mask total correlation image by defined voxels | :ref:`maskimg_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr_dfnd.4dfp.img |
| Fisher z transform total correlation | :ref:`rho2z_4dfp` | <FCdir>/ |br| <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr_dfnd_zfrm.4dfp.img |
| Compute zero-lag ROI-ROI correlation matrix (if number of ROIs <= 256) | :ref:`covariance` (-u, -o, -m0) | <FCdir>/ |br| <patid>_seed_regressors_CCR.dat |
generate Freesurfer masks for whole brain, WM, GM, CSF
Usage: Generate_FS_Masks_AZS.csh <parameters file> [instructions]
Examples:
Generate_FS_Masks_AZS.csh FCS_039_A_1.params ../uwrp_process_Stroke_SMG_Subjects.params
| Variable | Values | Description |
|---|---|---|
| patid | |patid_vals| | |patid_desc| |
| FSdir | |FSdir_vals| | |FSdir_desc| |
| target | |target_vals| | |target_desc| |