.. include:: ../global.rst fcMRI oriented scripts ====================== .. include:: ../notes/params-file-tip.rst .. _fcMRI_preproc_161012: fcMRI_preproc_161012.csh ------------------------- fcMRI preprocessing including nuisance variable regression .. attention:: :code:`fcMRI_preproc_161012` assumes successful completion of BOLD preprocessing (:ref:`cross_bold_pp_161012`). Usage: fcMRI_preproc_.csh [instructions file] Examples:: fcMRI_preproc_161012.csh VB16168.params **Required parameters** .. list-table:: :widths: 15 5 65 :header-rows: 1 * - 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** .. list-table:: :widths: 15 5 5 60 :header-rows: 1 * - 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** .. list-table:: :widths: 25 15 30 :class: wrap-rows :header-rows: 1 * - Step description - Function - Output * - Generate FS masks if they don't already exist - :ref:`Generate_FS_Masks_AZS` - **atlas/** |br| _orig_to__t4 |br| _FSWB_on__333.4dfp.img |br| _GM_on__333_comp_b60.4dfp.img |br| _(WM,CS)_erode_on__333_clus.4dfp.img * - Create conc file - :ref:`conc_4dfp` - **/** |br| $conc |br| or, [_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| [_faln_dbnd]_xr3d.FD |br| **atlas/** |br| [_faln_dbnd]_xr3d.FD.format (if $FDthresh) |br| _func_vols(.vals, .dat, .crit, .xmgr, .format) * - Create average censored image - :ref:`actmapf_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_ave.4dfp.img * - Compute defined mask and apply it - :ref:`compute_defined_4dfp`, :ref:`maskimg_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_dfnd.4dfp.img |br| **atlas/** |br| [_faln_dbnd]_xr3d_uwrp_atl_dfndm.4dfp.img * - Compute initial sd1 mean - :ref:`var_4dfp`, :ref:`qnt_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_sd1.4dfp.img * - Make timeseries zero mean - :ref:`var_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_uout.conc * - Make movement regressors for each bold run - :ref:`mat2dat`, :ref:`conc_4dfp`, :ref:`bandpass_4dfp`, :ref:`4dfptoascii` - **/** |br| [_faln_dbnd]_xr3d_dat.conc |br| [_faln_dbnd]_xr3d_dat_bpss.conc |br| __mov_regressors.dat * - Temporal bandpass filter using $bpss_params - :ref:`bandpass_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss.conc * - Make whole brain regressors including the 1st derivative - :ref:`qnt_4dfp` - **/** |br| _WB_regressors_dt.dat * - Make extra-axial CSF regressors (thresholded at $CSF_excl_lim) - :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` - **/** |br| _CSF_mask.4dfp.img |br| _CSF_dies.4dfp.img |br| _CSF_regressors.dat * - Make venticle regressors - :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` - **/** |br| _vent_mask.4dfp.img |br| _vent_dies.4dfp.img |br| _vent_regressors.dat * - Make white matter regressors - :ref:`maskimg_4dfp`, :ref:`qntv_4dfp` - **/** |br| _WM_mask.4dfp.img |br| _WM_dies.4dfp.img |br| _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 - - **/** |br| _nuisance_regressors.dat * - Remove nuisance regressors out of volumetric time series - :ref:`glm_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid.conc |br| [_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` - **/** |br| [_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` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g.conc * - Compute sd1 mean for blurred data if $blur - :ref:`var_4dfp`, :ref:`qnt_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g_sd1.4dfp.img |br| (mean reported to stdout) .. _seed_correl_161012: seed_correl_161012.csh ----------------------- compute multi-volume correlation maps .. attention:: :code:`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 [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** .. list-table:: :widths: 15 5 65 :header-rows: 1 * - 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** .. list-table:: :widths: 15 5 5 60 :header-rows: 1 * - 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** .. list-table:: :widths: 25 15 30 :class: wrap-rows :header-rows: 1 * - Step description - Function - Output * - Create (multi-volume) ROI image if $ROIlistfile or $ROIlist specified - :ref:`paste_4dfp` - * - Calculate seed (ROI) regressors - :ref:`qntm_4dfp` - **/** |br| _seed_regressors.dat |br| _seed_regressors.rec * - Compute total correlations - :ref:`glm_4dfp` (-t) - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g]_tcorr.4dfp.img * - Mask total correlation image by defined voxels - :ref:`maskimg_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g]_tcorr_dfnd.4dfp.img * - Fisher z transform total correlation - :ref:`rho2z_4dfp` - **/** |br| [_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g]_tcorr_dfnd_zfrm.4dfp.img * - Compute zero-lag ROI-ROI correlation matrix (if number of ROIs <= 256) - :ref:`covariance` (-u, -o, -m0) - **/** |br| _seed_regressors_CCR.dat .. _Generate_FS_Masks_AZS: Generate_FS_Masks_AZS.csh -------------------------- generate Freesurfer masks for whole brain, WM, GM, CSF Usage: Generate_FS_Masks_AZS.csh [instructions] Examples:: Generate_FS_Masks_AZS.csh FCS_039_A_1.params ../uwrp_process_Stroke_SMG_Subjects.params .. list-table:: :widths: 15 5 65 :class: wrap-row :header-rows: 1 * - Variable - Values - Description * - patid - |patid_vals| - |patid_desc| * - FSdir - |FSdir_vals| - |FSdir_desc| * - target - |target_vals| - |target_desc|