Deprecated scripts
cross_bold_pp
generic EPI (BOLD) pre-processing
Usage: cross_bold_pp_<version>.csh <params file> [instructions_file]
Examples:
cross_bold_pp_161012.csh VB16168.params
generic_cross_bold_pp_090115.csh VB16168.params
cross_bold_pp_130702.csh
Required parameters
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
irun |
<str array> |
list of run folders |
fstd |
<int array> |
list of scan numbers that map to run folders |
mprs |
<int array> |
list of mprage scan numbers |
target |
<img> |
atlas to be used for alignment |
go |
0,1 |
if calls should be executed (if 0, statements will only be printed, not executed) |
nx |
<int> |
number of voxels on the x-axis |
ny |
<int> |
number of voxels on the y-axis |
skip |
<int> |
number of pre-steady state frames |
TR_vol |
<flt> |
time per frame (s) |
TR_slc |
<flt> |
time per slice (s) (set to 0 to have it computed) |
epidir |
0,1 |
direction of EPI slices (0 = inferior to superior, 1 = superior to inferior) |
economy |
<int> |
level of removal for intermediate files created during execution (see table below) |
epi2atl |
0,1,2 |
if EPI to atlas transform is required (0 = no transform, 1 = transform to 333 space, 2 = skip to resampling step) |
normode |
0,1 |
if per-frame volume intensity should be modified |
day1_patid |
<str> |
patient directory for first session (if patid is not patient’s first session) |
day1_path |
<str> |
path to day1 atlas directory (required if day1_patid is set) |
uwrp_cmnd |
<str> |
script to use for unwarping |
rsam_cmnd |
<str> |
script to use for resampling |
Economy value |
Files to be removed |
---|---|
> 2 |
original bold run images |
> 3 |
frame-aligned images (_faln) |
> 4 |
cross-realigned avg images (_r3d_avg or xr3d_BC_avg if $BiasField) (only if $epi2atl == 0) |
Field map correction variables (required)
Variable |
Values |
Description |
---|---|---|
Option 1 (Measured field map - gradient echo) |
||
gre |
<int array> |
gradient echo measured field map scan numbers (magnitude image should be first, followed by phase image) |
delta |
<flt> |
difference between field map echo times (ms) |
TE_vol |
<int> |
echo time (ms) |
Option 2 (basis_opt field map) |
||
FMmean |
<img> |
mean field map image |
FMBases |
<img> |
?? |
Optional parameters
Tip
Although tse
and pdt2
are optional, you should specify one or the other if you have them in order to get a better registration to atlas.
Variable |
Values |
Default |
Description |
---|---|---|---|
tse |
<int array> |
list of tse scan numbers |
|
pdt2 |
<int array> |
list of proton-density weighted scan numbers |
|
scrdir |
<str> |
scratch directory to be |
|
sorted |
0,1 |
0 |
if dcm sort has already been run |
MB |
0,1 |
0 |
skip slice timing correction and debanding |
sx |
<int> |
1 |
unpacked x-dimension squeeze factor (unpack_4dfp) |
sy |
<int> |
1 |
unpacked y-dimension squeeze factor (unpack_4dfp) |
E4dfp |
0,1 |
0 |
if 4dfp files already exist (skips dcm_to_4dfp) |
use_anat_ave |
0,1 |
0 |
use _anat_ave epi image (default is _func_vols_ave) |
min_frames |
<int> |
240 |
minimum number of remaining frames after scrubbing for participant to be included |
interleave |
-S |
interleave |
sequential slice acquisition (frame_align_4dfp) |
MBfac |
<int> |
1 |
multiband factor |
anat_aveb |
<flt> |
0 |
run_dvar_4dfp preblur in mm (for small voxels, set to 10mm) |
anat_avet |
<flt> |
(compute) |
run_dvar_4dfp criterion (set excessively high to skip DVARS censoring) |
cross_day_nostretch |
0,1 |
0 |
disable stretch for cross-day transform |
Gad |
0,1 |
0 |
if gadolinium contrast was used |
Additional optional parameters
Warning
Only specify the following variables if the action is desired. They will happen if you specify them at all (even if you set them to 0).
Variable |
Description |
---|---|
goto_UNWARP |
immediately go to unwarp step |
epi_zflip |
flip z when unpacking (unpack_4dfp) |
Siemens_interleave |
enables Siemens interleave order (frame_align_4dfp) |
nounpack |
skips unpacking step |
Processing steps
Convert bold run dicoms to 4dfp format (dcm_to_4dfp)
Covert mosiac format to volume – if not $nounpack (unpack_4dfp)
Correct slice timing and odd/even slice intensities – if not $MB (frame_align_4dfp, deband_4dfp)
Motion correction via rigid body transform of each volume to reference frame (cross_realign3d_4dfp)
Compute and apply mode 1000 normalization (normalize_4dfp, scale_4dfp)
Extract/format movement data from on cross_realign3d_4dfp output (mat2dat)
Extract EPI first frame (anatomy) image (paste_4dfp)
Make func_vols_ave image with high movement frames removed (DVARS) (actmapf_4dfp)
Compute cross-session BOLD atlas transform – if $day1_patid specified for current patid (cross_day_imgreg_4dfp)
Convert MPRAGE dicoms to 4dfp format (dcm_to_4dfp)
Compute MPRAGE atlas transforms (mpr2atl1_4dfp with first mpr if $Gad, otherwise avgmpr_4dfp)
Compute EPI atlas transform
(Show/Hide Details)
Make atlas transformed EPI anat_ave and t2w in 111, 222, and 333 atlas space (t4img_4dfp)
Compute field mapping correction ($uwrp_cmnd)
Compute and apply unwarped epi to atlas transform (imgreg_4dfp, t4_mul, t4img_4dfp)
Resample unwarped images ($rsam_cmnd)
Make average atlas-aligned, unwarped image (actmapf_4dfp)
cross_bold_pp_121215.csh
Required parameters
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
target |
<img> |
atlas to be used for alignment |
irun |
<str array> |
list of run folders |
fstd |
<int array> |
list of scan numbers that map to run folders |
mprs |
<int array> |
list of mprage scan numbers |
go |
0,1 |
if calls should be executed (if 0, statements will only be printed, not executed) |
nx |
<int> |
number of voxels on the x-axis |
ny |
<int> |
number of voxels on the y-axis |
skip |
<int> |
number of pre-steady state frames |
TR_vol |
<flt> |
time per frame (s) |
TR_slc |
<flt> |
time per slice (s) (set to 0 to have it computed) |
epidir |
0,1 |
direction of EPI slices (0 = inferior to superior, 1 = superior to inferior) |
economy |
<int> |
level of removal for intermediate files created during execution (see table below) |
epi2atl |
0,1,2 |
if EPI to atlas transform is required (0 = no transform, 1 = transform to 333 space, 2 = skip to resampling step) |
normode |
0,1 |
if per-frame volume intensity should be modified |
Economy value |
Files to be removed |
---|---|
> 2 |
original bold images |
> 3 |
frame-aligned images (_faln) |
> 4 |
debanded images (_faln_dbnd) (only if $epi2atl == 0) |
> 6 |
normalized images (_norm) |
Optional parameters
Tip
Although tse
and pdt2
are optional, you should specify one or the other if you have them in order to get a better registration to atlas.
Variable |
Values |
Default |
Description |
---|---|---|---|
tse |
<int array> |
list of tse scan numbers |
|
pdt2 |
<int array> |
list of proton-density weighted scan numbers |
|
t1w |
<int array> |
list of t1w scan numbers |
|
scrdir |
<str> |
scratch directory to be |
|
to_MNI152 |
0,1 |
0 |
transform to MNI152 atlas space |
day1_patid |
<str> |
patient directory for first session (if patid is not patient’s first session) |
|
day1_path |
<str> |
path to day1 atlas directory (required if day1_patid is set) |
|
sorted |
0,1 |
0 |
if dcm sort has already been run |
Additional optional parameters
Warning
Only specify the following variables if the action is desired. They will happen if you specify them at all (even if you set them to 0).
Variable |
Description |
---|---|
Siemens_interleave |
enables Siemens interleave order (frame_align_4dfp) |
Processing steps
Convert bold run dicoms to 4dfp format (dcm_to_4dfp)
Covert mosiac format to volume (unpack_4dfp)
Correct slice timing and odd/even slice intensities (frame_align_4dfp, deband_4dfp)
Motion correction via rigid body transform of each volume to reference frame (cross_realign3d_4dfp)
Compute and apply mode 1000 normalization (normalize_4dfp, scale_4dfp)
Extract/format movement data from on cross_realign3d_4dfp output (mat2dat)
Extract EPI first frame (anatomy) image (paste_4dfp)
Move anatomy image (anat_ave) to atlas directory
Compute cross-session BOLD atlas transform if $day1_patid specified for current patid (cross_day_imgreg_4dfp)
Convert MPRAGE dicoms to 4dfp format (dcm_to_4dfp)
Compute MPRAGE atlas transforms (avgmpr_4dfp)
Compute EPI atlas transform
(Show/Hide Details)
Make atlas transformed EPI anat_ave in 111, 222, and 333 (711-2B or MNI152 if $to_MNI152) atlas space (t4img_4dfp)
Make cross-realigned atlas-transformed resampled BOLD 4dfp stacks (t4_xr3d_4dfp)
generic_cross_bold_pp_090115
Required parameters
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
irun |
<str array> |
list of run folders |
fstd |
<int array> |
list of scan numbers that map to run folders |
mprs |
<int array> |
list of mprage scan numbers |
target |
<img> |
atlas to be used for alignment |
go |
0,1 |
if calls should be executed (if 0, statements will only be printed, not executed) |
nx |
<int> |
number of voxels on the x-axis |
ny |
<int> |
number of voxels on the y-axis |
skip |
<int> |
number of pre-steady state frames |
TR_vol |
<flt> |
time per frame (s) |
TR_slc |
<flt> |
time per slice (s) (set to 0 to have it computed) |
epidir |
0,1 |
direction of EPI slices (0 = inferior to superior, 1 = superior to inferior) |
economy |
<int> |
level of removal for intermediate files created during execution (see table below) |
epi2atl |
0,1,2 |
if EPI to atlas transform is required (0 = no transform, 1 = transform to 333 space, 2 = skip to resampling step) |
normode |
0,1 |
if per-frame volume intensity should be modified |
Economy value |
Files to be removed |
---|---|
> 2 |
original bold images |
> 3 |
frame-aligned images (_faln) |
> 4 |
debanded images (_faln_dbnd) (only if $epi2atl == 0) |
> 6 |
normalized images (_norm) |
Optional parameters
Tip
Although tse
and pdt2
are optional, you should specify one or the other if you have them in order to get a better registration to atlas.
Variable |
Values |
Default |
Description |
---|---|---|---|
tse |
<int array> |
list of tse scan numbers |
|
pdt2 |
<int array> |
list of proton-density weighted scan numbers |
|
t1w |
<int array> |
list of t1w scan numbers |
|
scrdir |
<str> |
scratch directory to be |
|
sorted |
0,1 |
0 |
if dcm sort has already been run |
MB |
0,1 |
0 |
skip slice timing correction and debanding |
sx |
<int> |
1 |
unpacked x-dimension squeeze factor (unpack_4dfp) |
sy |
<int> |
1 |
unpacked y-dimension squeeze factor (unpack_4dfp) |
E4dfp |
0,1 |
0 |
if 4dfp files already exist (skips dcm_to_4dfp) |
interleave |
-S |
sequential slice acquisition (frame_align_4dfp) |
|
MBfac |
<int> |
1 |
multiband factor |
day1_patid |
<str> |
patient directory for first session (if patid is not patient’s first session) |
|
day1_path |
<str> |
path to day1 atlas directory (required if day1_patid is set) |
|
cross_day_nostretch |
0,1 |
0 |
disable stretch for cross-day transform |
Gad |
0,1 |
0 |
if gadolinium contrast was used |
Additional optional parameters
Warning
Only specify the following variables if the action is desired. They will happen if you specify them at all (even if you set them to 0).
Variable |
Description |
---|---|
epi_zflip |
flip z when unpacking (unpack_4dfp) |
Siemens_interleave |
enables Siemens interleave order (frame_align_4dfp) |
nounpack |
skips unpacking step |
Processing steps
Convert bold run dicoms to 4dfp format (dcm_to_4dfp)
Covert mosiac format to volume – if not $nounpack (unpack_4dfp)
Correct slice timing and odd/even slice intensities – if not $MB (frame_align_4dfp, deband_4dfp)
Motion correction via rigid body transform of each volume to reference frame (cross_realign3d_4dfp)
Compute and apply mode 1000 normalization (normalize_4dfp, scale_4dfp)
Extract/format movement data from on cross_realign3d_4dfp output (mat2dat)
Extract EPI first frame (anatomy) image (paste_4dfp)
Move anatomy image (anat_ave) to atlas directory
Compute cross-session BOLD atlas transform if $day1_patid specified for current patid (cross_day_imgreg_4dfp)
Convert MPRAGE dicoms to 4dfp format (dcm_to_4dfp)
Compute MPRAGE atlas transforms (mpr2atl1_4dfp with first mpr if $Gad, otherwise avgmpr_4dfp)
Compute EPI to atlas transform
Compute EPI atlas transform
(Show/Hide Details)
Make atlas transformed EPI anat_ave in 111, 222, and 333 atlas space (t4img_4dfp)
Make cross-realigned atlas-transformed resampled BOLD 4dfp stacks (t4_xr3d_4dfp)
fcMRI_preproc
fcMRI preprocessing including nuisance variable regression.
Attention
fcMRI_preproc
assumes successful completion of BOLD preprocessing (cross_bold_pp).
Usage: fcMRI_preproc_<version>.csh <params file> [instructions file]
Examples:
fcMRI_preproc_161012.csh VB16168.params
fcMRI_preproc_090115.csh VB16168.params
fcMRI_preproc_140413.csh
Required parameters
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
srcdir |
<str> |
source directory path (contains run directories) |
workdir |
<str> |
working directory path |
TR_vol |
<flt> |
time per frame (s) |
skip |
<int> |
number of pre-steady state frames |
fcbolds |
<array> |
list of bold run folders |
Optional parameters
Variable |
Values |
Default |
Description |
---|---|---|---|
FCdir |
<str> |
FCmaps |
output directory name |
anat_aveb |
<flt> |
10 |
run_dvar_4dfp preblur in mm (for small voxels, set to 10mm) |
anat_avet |
<flt> |
7 |
run_dvar_4dfp criterion |
FWHM |
<int> |
6 |
full-width half maximum for spatial blur |
MB |
0,1 |
0 |
skip slice timing correction and debanding |
conc |
<str> |
pre-existing conc file to use |
|
task_regressor |
<str> |
optional externally supplied task regressor |
|
noGSR |
1 |
0 |
suppress global signal (WB) regression |
Processing steps
Create conc file (conc_4dfp) and move it to FCdir
Compute defined mask and apply it (compute_defined_4dfp, maskimg_4dfp)
Compute frame censoring (DVARS) (run_dvar_4dfp)
Make movement regressors for each bold run (mat2dat)
Make whole brain regressors including the 1st derivative (qnt_4dfp)
Make ventricle and bilateral white matter regressors and their derivatives (qnt_4dfp)
Paste nuisance regressors together (including task_regressor if supplied)
Remove nuisance regressors out of volumetric time series (glm_4dfp)
Temporal bandpass filter with bh = .1 and oh = 2 (bandpass_4dfp)
Spatial blur with f_half = 4.413/$FWHM (gauss_4dfp)
fcMRI_preproc_130715.csh
Params file variables
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
srcdir |
<str> |
source directory path (contains run directories) |
fcbolds |
<array> |
list of bold run folders |
Instructions file variables
Variable |
Values |
Description |
---|---|---|
FCdir |
<str> |
output directory name |
FSdir |
<str> |
freesurfer directory containing mri/aparc+aseg.mgz |
MB |
0,1 |
skip slice timing correction and debanding |
conc |
<str> |
pre-existing conc file to use |
task_regressor |
<str> |
optional externally supplied task regressor |
noGSR |
1 |
suppress global signal (WB) regression |
anat_aveb |
<flt> |
run_dvar_4dfp preblur in mm (for small voxels, set to 10mm) |
anat_avet |
<flt> |
run_dvar_4dfp criterion |
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) |
fmtfile |
<str> |
format file |
bpss_params |
<array> |
options for bandpass_4dfp (only -E,M,F specified by default; no default bands) |
blur |
<flt> |
f_half for spatial blur |
Processing steps
Generate FS masks (results in ../atlas) (Generate_FS_Masks_AZS.csh)
Create conc file (conc_4dfp) and move it to FCdir
Compute frame censoring (DVARS) (run_dvar_4dfp) and create avg censored image – only if no $fmtfile specified
Compute defined mask and apply it (compute_defined_4dfp, maskimg_4dfp)
Make timeseries zero mean (var_4dfp)
Make movement regressors for each bold run (mat2dat)
Temporal bandpass filter using $bpss_params (bandpass_4dfp)
Make whole brain regressors including the 1st derivative (qnt_4dfp)
Make extra-axial CSF regressors (maskimg_4dfp)
Make venticle movement_regressors (qntv_4dfp)
Make white matter regressors (qntv_4dfp)
Paste nuisance regressors together (including task_regressor if supplied)
Pass final set of nuisance regressors (omitting WB and WB derivative) through covariance -D250
Remove nuisance regressors out of volumetric time series (glm_4dfp)
Spatial blur with f_half = $blur if specified (gauss_4dfp)
fcMRI_preproc_090115H.csh
Hallquist compliant version of fcMRI_preproc_090115.csh
Params file variables
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
srcdir |
<str> |
source directory path (contains run directories) |
workdir |
<str> |
working directory path |
fcbolds |
<array> |
list of bold run folders |
Instructions file variables
Variable |
Values |
Description |
---|---|---|
FCdir |
<str> |
output directory name |
MB |
0,1 |
skip slice timing correction and debanding |
conc |
<str> |
pre-existing conc file to use |
task_regressor |
<str> |
optional externally supplied task regressor |
noGSR |
1 |
suppress global signal (WB) regression |
noWM |
1 |
supress WM regression |
movement_regressors |
raw,bpss,none |
?? |
Processing steps
Create conc file (conc_4dfp) and move it to FCdir
Compute defined mask and apply it (compute_defined_4dfp, maskimg_4dfp)
Spatial blur with f_half = .735452 (gauss_4dfp)
Temporal bandpass filter with bh = .1 and oh = 2 (bandpass_4dfp)
Make movement regressors for each bold run (mat2dat) (if $movement_regressors is not “none”)
Make whole brain, ventricle, and bilateral white matter regressors (qnt_4dfp)
Paste nuisance regressors together (including task_regressor if supplied)
Pass final set of nuisance regressors (omitting WB and WB derivative) through covariance -D500
Remove nuisance regressors out of volumetric time series (glm_4dfp)
fcMRI_preproc_090115.csh
Params file variables
Variable |
Values |
Description |
---|---|---|
patid |
<str> |
unique identifier for current subject/session |
srcdir |
<str> |
source directory path (contains run directories) |
workdir |
<str> |
working directory path |
fcbolds |
<array> |
list of bold run folders |
Instructions file variables
Variable |
Values |
Description |
---|---|---|
FCdir |
<str> |
output directory name |
MB |
0,1 |
skip slice timing correction and debanding |
conc |
<str> |
pre-existing conc file to use |
task_regressor |
<str> |
optional externally supplied task regressor |
noGSR |
1 |
suppress global signal (WB) regression |
Processing steps
Create conc file (conc_4dfp) and move it to FCdir
Compute defined mask and apply it (compute_defined_4dfp, maskimg_4dfp)
Spatial blur with f_half = .735452 (gauss_4dfp)
Temporal bandpass filter with bh = .1 and oh = 2 (bandpass_4dfp)
Make movement regressors for each bold run (mat2dat)
Make whole brain, ventricle, and bilateral white matter regressors (qnt_4dfp)
Paste nuisance regressors together (including task_regressor if supplied)
Remove nuisance regressors out of volumetric time series (glm_4dfp)
seed_correl
compute multi-volume correlation maps
Attention
seed_correl
assumes successful completion of BOLD preprocessing (cross_bold_pp) and fcMRI preprocessing (fcMRI_preproc).
Usage: seed_correl_<version>.csh <parameters file> [instructions] [options]