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> |
options for bandpass_4dfp (only -E,M,F specified by default; no default bands) |
|
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 |
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 |
<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 |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_ave.4dfp.img |
|
Compute defined mask and apply it |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_dfnd.4dfp.img atlas/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_dfndm.4dfp.img |
|
Compute initial sd1 mean |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_sd1.4dfp.img |
|
Make timeseries zero mean |
<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 |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss.conc |
|
Make whole brain regressors including the 1st derivative |
<FCdir>/ <patid>_WB_regressors_dt.dat |
|
Make extra-axial CSF regressors (thresholded at $CSF_excl_lim) |
<FCdir>/ <patid>_CSF_mask.4dfp.img <patid>_CSF_dies.4dfp.img <patid>_CSF_regressors.dat |
|
Make venticle regressors |
<FCdir>/ <patid>_vent_mask.4dfp.img <patid>_vent_dies.4dfp.img <patid>_vent_regressors.dat |
|
Make white matter regressors |
<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 |
<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 |
<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 |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid_g<blur>.conc |
|
Compute sd1 mean for blurred data if $blur |
<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> |
options for bandpass_4dfp (only -E,M,F specified by default; no default bands) |
|
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 |
||
Calculate seed (ROI) regressors |
<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 |
<FCdir>/ <patid>[_faln_dbnd]_xr3d_uwrp_atl_bpss_resid[_g<blur>]_tcorr_dfnd.4dfp.img |
|
Fisher z transform total correlation |
<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 |