fcMRI oriented scripts

Tip

For more information on script inputs, see Params/Instructions files.

fcMRI_preproc_161012.csh

fcMRI preprocessing including nuisance variable regression

Attention

fcMRI_preproc_161012 assumes successful completion of BOLD preprocessing (cross_bold_pp_161012.csh).

Usage: fcMRI_preproc_<version>.csh <params file> [instructions file]

Examples:

fcMRI_preproc_161012.csh VB16168.params

Required parameters

Variable Values Description
patid <str> unique identifier for current subject/session
target <img> atlas to be used for alignment
FSdir <str> freesurfer directory containing mri/aparc+aseg.mgz
srcdir <str> source directory path (contains run directories)
fcbolds <array> list of bold run folders
TR_vol <flt> time per frame (s)
CSF_lcube <int> cube dimension (in voxels) used by qntv_4dfp for CSF (recommended: 3)
CSF_sd1t <flt> threshold CSF sd1 image (recommended: 25)
CSF_svdt <flt> limit regressor covariance condition number to (1/{})^2 for CSF (recommended: .2)
WM_lcube <int> cube dimension (in voxels) used by qntv_4dfp for WM (recommended: 5)
WM_svdt <flt> limit regressor covariance condition number to (1/{})^2 for WM (recommended: .15)

Optional parameters

Variable Values Default Description
FCdir <str> FCmaps output directory name
day1_patid <str>   patient directory for first session (if patid is not patient’s first session)
MB 0,1 0 skip slice timing correction and debanding
blur <flt> no blur f_half for spatial blur
bpss_params <array>   additional options to use for bandpass filtering (-E,M,F already specified), e.g. ( -bh .1 -oh 2 )
conc <str>   pre-existing conc file to use
fmtfile <str>   format file
FDthresh <flt>   frame displacement thresholds
FDtype 1,2 1 frame displacement calculation (1 = absolute value, 2 = squares)
anat_aveb <flt> 0 run_dvar_4dfp preblur in mm (for small voxels, set to 10mm)
anat_avet <flt> (compute) run_dvar_4dfp criterion
min_frames <int> numframes / 2 minimum number of remaining frames after scrubbing for participant to be included
CSF_excl_lim <flt> 0.126 mask threshold for CSF
task_regressor <str>   optional externally supplied task regressor
noGSR 1 0 suppress global signal (WB) regression

Processing steps

Step description Function Output
Generate FS masks if they don’t already exist Generate_FS_Masks_AZS.csh atlas/
<patid>_orig_to_<target>_t4
<patid>_FSWB_on_<target>_333.4dfp.img
<patid>_GM_on_<target>_333_comp_b60.4dfp.img
<patid>_(WM,CS)_erode_on_<target>_333_clus.4dfp.img
Create conc file conc_4dfp <FCdir>/
$conc
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, run_dvar_4dfp movement/
<patid>[_faln_dbnd]_xr3d.FD
atlas/
<patid>[_faln_dbnd]_xr3d.FD.format (if $FDthresh)
<patid>_func_vols(.vals, .dat, .crit, .xmgr, .format)
Create average censored image actmapf_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_ave.4dfp.img
Compute defined mask and apply it compute_defined_4dfp, maskimg_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_dfnd.4dfp.img
atlas/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_dfndm.4dfp.img
Compute initial sd1 mean var_4dfp, qnt_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_sd1.4dfp.img
Make timeseries zero mean var_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_uout.conc
Make movement regressors for each bold run mat2dat, conc_4dfp, bandpass_4dfp, 4dfptoascii <FCdir>/
<patid>[_faln_dbnd]_xr3d_dat.conc
<patid>[_faln_dbnd]_xr3d_dat_bpss.conc
<patid>_<patid>_mov_regressors.dat
Temporal bandpass filter using $bpss_params bandpass_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss.conc
Make whole brain regressors including the 1st derivative qnt_4dfp <FCdir>/
<patid>_WB_regressors_dt.dat
Make extra-axial CSF regressors (thresholded at $CSF_excl_lim) maskimg_4dfp, qntv_4dfp <FCdir>/
<patid>_CSF_mask.4dfp.img
<patid>_CSF_dies.4dfp.img
<patid>_CSF_regressors.dat
Make venticle regressors maskimg_4dfp, qntv_4dfp <FCdir>/
<patid>_vent_mask.4dfp.img
<patid>_vent_dies.4dfp.img
<patid>_vent_regressors.dat
Make white matter regressors maskimg_4dfp, qntv_4dfp <FCdir>/
<patid>_WM_mask.4dfp.img
<patid>_WM_dies.4dfp.img
<patid>_WM_regressors.dat
Paste nuisance regressors (mov, CSF, vent, WM, task) together and run covariance analysis covariance (-D250)  
Paste together WB and WB derivative, and covaried nuissance regressors   <FCdir>/
<patid>_nuisance_regressors.dat
Remove nuisance regressors out of volumetric time series glm_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid.conc
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_coeff.4dfp.img
Compute sd1 mean for bandpass-filtered and nuisance regressed data var_4dfp, qnt_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_sd1.4dfp.img
(comparison to initial WB mean reported to stdout)
Spatial blur with f_half = $blur if specified gauss_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g<blur>.conc
Compute sd1 mean for blurred data if $blur var_4dfp, qnt_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g<blur>_sd1.4dfp.img
(mean reported to stdout)

seed_correl_161012.csh

compute multi-volume correlation maps

Attention

seed_correl_161012 assumes successful completion of BOLD preprocessing (cross_bold_pp_161012.csh) and fcMRI preprocessing (fcMRI_preproc_161012.csh).

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 <str> unique identifier for current subject/session
ROIdir <str> directory containing ROI image(s)
skip <int> number of pre-steady state frames

ROI specification variables (required)

Variable Values Description
Option 1
ROIimg <str> base filename for single ROI image
Option 2
ROIlist <str array> list of base filenames for ROI images
Option 3
ROIlistfile <str> list file (.lst) of base filenames for ROI image

Optional variables

Variable Values Default Description
FCdir <str> FCmaps output directory name
MB 0,1 0 skip slice timing correction and debanding
blur <flt> no blur f_half for spatial blur
bpss_params <array>   additional options to use for bandpass filtering (-E,M,F already specified), e.g. ( -bh .1 -oh 2 )
conc <str>   pre-existing conc file to use
fmtfile <str>   format file

Processing Steps

Step description Function Output
Create (multi-volume) ROI image if $ROIlistfile or $ROIlist specified paste_4dfp  
Calculate seed (ROI) regressors qntm_4dfp <FCdir>/
<patid>_seed_regressors.dat
<patid>_seed_regressors.rec
Compute total correlations glm_4dfp (-t) <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr.4dfp.img
Mask total correlation image by defined voxels maskimg_4dfp <FCdir>/
<patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr_dfnd.4dfp.img
Fisher z transform total correlation rho2z_4dfp <FCdir>/
<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) covariance (-u, -o, -m0) <FCdir>/
<patid>_seed_regressors_CCR.dat

Generate_FS_Masks_AZS.csh

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 <str> unique identifier for current subject/session
FSdir <str> freesurfer directory containing mri/aparc+aseg.mgz
target <img> atlas to be used for alignment