fMRI oriented scripts
Tip
For more information on script inputs, see Params/Instructions files.
cross_bold_pp_161012.csh
generic EPI (BOLD) pre-processing
Usage: cross_bold_pp_161012.csh <params file> [instructions_file]
Examples:
cross_bold_pp_161012.csh VB16168.params
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 |
inpath |
<str> |
top-level directory for raw DICOM data (i.e. directory containing study folders if $sorted) |
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) |
FDthresh |
<flt> |
frame displacement thresholds |
normode |
0,1 |
if per-frame volume intensity should be modified |
dwell |
<flt> |
EPI dwell time (echo spacing) (ms) |
ped |
x,x-,y,y-,z,z- |
EPI phase encoding direction |
rsam_cmnd |
<str> |
script to use for resampling (recommended: one_step_resample.csh) |
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 parameters (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 (Measured field map - spin echo) |
||
sefm |
<int array> |
spin echo measured field maps |
TE_vol |
<int> |
echo time (ms) |
Option 3 (Mean field map) |
||
FMmean |
<img> |
mean field map image |
Option 4 (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 |
|
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) |
|
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 |
sequential slice acquisition (frame_align_4dfp) |
|
seqstr |
<str> |
specify [MB] slice sequence (counting from 1) as a comma-separated (no spaces) integer string (if non-standard interleaving) |
|
MBfac |
<int> |
1 |
multiband factor |
lomotil |
1-6 |
lowpass filter for specified motion parameter (mat2dat -l), used for filtered FD (set to 2 for y direction) |
|
BiasField |
0,1 |
0 |
perform bias field correction |
FDtype |
1,2 |
1 |
frame displacement calculation (1 = absolute value, 2 = squares) |
anat_aveb |
<flt> |
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
Step description |
Function |
Output |
|---|---|---|
Convert bold run DICOM data to 4dfp format |
||
Convert mosaic format to volume (if not $nounpack) |
bold<irun>/ <patid>_b<irun>.4dfp.img |
|
Correct slice timing and odd/even slice intensities (if not $MB) |
bold<irun>/ <patid>_b<irun>_faln.4dfp.img <patid>_b<irun>_faln_dbnd.4dfp.img |
|
Motion correction via rigid body transform of each volume to reference frame |
bold<irun>/ <patid>_b<irun>[_faln_dbnd]_xr3d.4dfp.img <patid>_b<irun>[_faln_dbnd]_r3d_avg.4dfp.img <patid>_b<irun>[_faln_dbnd]_xr3d.mat |
|
Bias field correction (if $BiasField) |
FSL bet, FSL fast, extend_fast_4dfp |
bold<irun>/ <patid>_b<irun>[_faln_dbnd]_xr3d_BC_avg.4dfp.img atlas/ <patid>[_faln_dbnd]_xr3d_avg_brain.nii.gz <patid>[_faln_dbnd]_xr3d_avg_brain_restore(.4dfp.img, .nii.gz) |
Compute and apply within-run mode 1000 normalization |
bold<irun>/ <patid>_b<irun>[_faln_dbnd]_xr3d[_BC]_norm.4dfp.img |
|
Extract/format movement data from cross-realign output |
movement/ <patid>_b<irun>[_faln_dbnd]_xr3d(.dat, .ddat, .rdat) |
|
Extract EPI first frame (anatomy) image and create functional volume conc file |
atlas/ <patid>_anat_ave.4dfp.img <patid>_func_vols.conc |
|
Compute high movement frames using FD (if $FDthresh specified) and DVARS (stops here if $min_frames criteria not met) |
FD.awk (using .ddat movement file), 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) |
Make func_vols_ave image with high movement frames removed |
atlas/ <patid>_func_vols_ave.4dfp.img |
|
Compute cross-session BOLD atlas transform if $day1_patid specified (then skips to applying EPI transform step) |
atlas/ <patid>_anat_ave_to_<target>_t4 (and other intermediate t4 files) |
|
Convert MPRAGE DICOM data to 4dfp format (if not $E4dfp) |
atlas/ <patid>_mpr#.4dfp.img |
|
Convert MPRAGE images to tranverse orientation (if not already) |
atlas/ <patid>_mpr#T.4dfp.img |
|
Compute MPRAGE average |
atlas/ <patid>_mpr_n#.4dfp.img |
|
Create transverse t2w image (if $tse or $pdt) |
collate_slice_4dfp if $tse, extract_frame_4dfp (second frame) if $pdt, C2T_4dfp or S2T_4dfp |
atlas/ <patid>_t2w[T].4dfp.img |
Compute EPI to atlas transform |
epi2mpr2atl2_4dfp if neither $tse nor $pdt, otherwise epi2t2w2mpr2atl2_4dfp |
atlas/ <patid>_anat_ave_to_<target>_t4 (and other intermediate t4 files) |
Make atlas transformed EPI average image and t2w in 111, 222, and 333 atlas space |
atlas/ <patid>_(anat|func_vols)_ave_on_<target>_111.4dfp.img <patid>_(anat|func_vols)_ave_on_<target>_222.4dfp.img <patid>_(anat|func_vols)_ave_on_<target>_333.4dfp.img |
|
Compute field mapping correction |
unwarp/ <patid>_(anat|func_vols)_ave_uwrp.4dfp.img |
|
Compute and apply unwarped epi to atlas transform |
unwarp/ <patid>_(anat|func_vols)_ave_uwrp_on_<target>_111.4dfp.img <patid>_(anat|func_vols)_ave_uwrp_on_<target>_222.4dfp.img <patid>_(anat|func_vols)_ave_uwrp_on_<target>_333.4dfp.img |
|
One-step resample unwarped images |
$rsam_cmnd |
bold<irun>/ <patid>_[_faln_dbnd]_xr3d_uwrp_atl.4dfp.img |
fmri_unwarp_170616.tcsh
distortion correction wrapper script for fMRI preprocessing
Measured field map
Usage: fmri_unwarp_170616.tcsh -map <patid> <epi> <mag> <phase> <dwell> <te> <ped> <delta>
Variable |
Values |
Description |
|---|---|---|
patid |
<str> |
unique identifier for current subject/session |
epi |
<4dfp img> |
EPI anat image (_anat_ave or _func_vols_ave) |
mag |
<nifti img> |
magnitude field map image |
phase |
<nifti img> |
phase field map image |
dwell |
<flt> |
EPI dwell time (echo spacing) (ms) |
te |
<int> |
echo time (ms) |
ped |
x,x-,y,y-,z,z- |
EPI phase encoding direction |
delta |
<flt> |
difference between field map echo times (ms) (required only for gradient-echo field map) |
Mean field map
Usage: fmri_unwarp_170616.tcsh -mean <epi> <FMmean> <epi_to_atl_t4> <dwell> <ped>
Variable |
Values |
Description |
|---|---|---|
epi |
<4dfp img> |
EPI anat image (_anat_ave or _func_vols_ave) |
FMmean |
<img> |
mean field map image |
epi_to_atl_t4 |
<t4 file> |
EPI to atlas t4 file |
dwell |
<flt> |
EPI dwell time (echo spacing) (ms) |
ped |
x,x-,y,y-,z,z- |
EPI phase encoding direction |
basis_opt field map
Usage: fmri_unwarp_170616.tcsh -basis <epi> <t2w> <FMmean> <FMbases> <epi_to_t2w_t4> <epi_to_atl_t4> <dwell> <ped> <nbasis> [t2w brain mask]
Variable |
Values |
Description |
|---|---|---|
epi |
<4dfp img> |
EPI anat image (_anat_ave or _func_vols_ave) |
t2w |
<4dfp img> |
structural 4dfp image (can be t2w or mpr) |
FMmean |
<img> |
mean field map image |
epi_to_t2w_t4 |
<t4 file> |
EPI to T2-weighted t4 file |
epi_to_atl_t4 |
<t4 file> |
EPI to atlas t4 file |
dwell |
<flt> |
EPI dwell time (echo spacing) (ms) |
ped |
x,x-,y,y-,z,z- |
EPI phase encoding direction |
nbasis |
<int> |
?? |
N.B.: with option -basis, basis_opt optimizes the <dwell> value (aka, echo spacing) by default
sefm_pp_AZS.csh
merge AP/PA into one image and run topup to derive field map
Usage: sefm_pp_AZS.csh <params file> [instructions file]
Examples:
sefm_pp_AZS.csh PSQ0001_s1.params ../PSQ_study.params
Variable |
Values |
Description |
|---|---|---|
patid |
<str> |
unique identifier for current subject/session |
sefm |
<int array> |
spin echo measured field maps |
sorted |
1 |
if dcm sort has already been run (must be sorted) |
one_step_resample.csh
one step resampling with support for bias field correction
Usage: one_step_resample.csh <parameters file> [instructions]
Examples:
one_step_resample.csh VB16168.params
Params variables
Variable |
Values |
Description |
|---|---|---|
patid |
<str> |
unique identifier for current subject/session |
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) |
irun |
<str array> |
list of run folders |
Instructions variables
Variable |
Values |
Description |
|---|---|---|
use_anat_ave |
0,1 |
use _anat_ave epi image (default is _func_vols_ave) |
outres |
111,222,333 |
output resolution (default = 333) |
target |
<img> |
atlas to be used for alignment |
MB |
0,1 |
skip slice timing correction and debanding |
BiasField |
0,1 |
perform bias field correction |
epi2mpr2atlv_4dfp
EPI \(\rightarrow\) T1W \(\rightarrow\) atlas
Usage: epi2mpr2atlv_4dfp <epi_anat> <mpr_anat> [useold] [atlas target [711-2? OR -T<target including path>] [-S<atlas space>] [noinit]
Examples:
epi2mpr2atlv_4dfp stem9_anat_ave stem9_654-3 useold 711-2C
epi2mpr2atlv_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B
Options
useold |
inhibits re-computation of all t4 files |
noinit |
inhibits reinitialization of epi->mpr t4 files |
-T<str> |
atlas target (specified string should include path) (default is 711-2B) |
-S |
specifies the atlas space (requires -T) (currently only 711-2B is supported) |
N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3
N.B.: All named images must be in either ANALYZE or 4dfp format. ANALYZE will be converted to 4dfp
epi2t2w2mpr2atlv_4dfp
EPI \(\rightarrow\) T2W \(\rightarrow\) T1W \(\rightarrow\) atlas (8 parameter cross-modal; for “low” res fMRI)
Usage: epi2t2w2mpr2atlv_4dfp <epi_anat> <t2w_anat> <mpr_anat> [useold] [atlas_target]
Examples:
epi2t2w2mpr2atlv_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 useold 711-2Y
Step description |
Function |
Inputs |
Output |
|---|---|---|---|
Compute MPR to atlas transform |
mpr2atl_4dfp |
${mpr}_to_${target}_t4 |
|
Blur images |
t_half = 1.1 |
${mpr}_g11 ${t2w}_g11 ${epi}_g11 |
|
Compute MPR brain mask |
msktgen_4dfp |
${mpr}_mskt |
|
Compute (iteratively) T2w to MPR transform |
imgreg_4dfp, using blurred (*_g11) images as source/target |
w/ unmasked mpr (source_mask = none) modes[1] = 1024 + 3 w/ masked mpr (source_mask = ${mpr}_mskt) modes[2] = 1024 + 3 modes[3] = 2048 + 3 + 8 + 64 modes[4] = 8192 + 2048 + 3 + 8 + 64 |
${t2w}_to_${mpr}_t4 |
Compute EPI brain mask |
gauss_4dfp, imgmax_4dfp, img2msk_4dfp, maskimg_4dfp |
f_half = .3 threshold = .2 * max(blurred epi) |
${epi}_msk |
Compute EPI (iteratively) to T2w transform |
imgreg_4dfp, using blurred (*_g11) images as source/target |
w/ original epi (source_msk = none) modes[1] = 1024 + 3 w/ masked epi (source_msk=${epi}_msk) modes[2] = 1024 + 3 modes[3] = 3072 + 3 + 8 + 64 modes[4] = 8192 + 2048 + 3 + 8 + 64 |
${epi}_to_${t2w}_t4 |
Combine transforms |
${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 |
${t2w}_to_${target}_t4 ${epi}_to_${target}_t4 ${epi}_to_${mpr}_t4 |
N.B.: Any argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3
N.B.: All named images must be in either ANALYZE or 4dfp format. ANALYZE will be converted to 4dfp
N.B.: ‘useold’ instructs epi2t2w2mpr2atlv_4dfp to use existing t4 files
N.B.: The default atlas_target is 711-2B
epi2t2w2mpr2atl1_4dfp
EPI \(\rightarrow\) T2W \(\rightarrow\) T1W \(\rightarrow\) atlas (9 parameter cross-modal; for “high” res fMRI)
Usage: epi2t2w2mpr2atl1_4dfp <epi_anat> <t2w_anat> <mpr_anat> [useold] [711-2? OR -T<Target including path>] [-S<atlas space>]
Examples:
epi2t2w2mpr2atl1_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 711-2B
epi2t2w2mpr2atl1_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B
Step description |
Function |
Inputs |
Output |
|---|---|---|---|
Compute MPR to atlas transform |
mpr2atl_4dfp |
${mpr}_to_${target}_t4 |
|
Compute MPR brain mask |
msktgen_4dfp |
${mpr}_mskt |
|
Compute (iteratively) T2w to MPR transform |
w/ original mpr (source_mask = none) modes[1] = 1024 + 3 w/ masked mpr (source_mask = ${mpr}_mskt) modes[2] = 1024 + 3 modes[3] = 2048 + 3 + 8 + 64 modes[4] = 8192 + 2048 + 3 + 8 |
${t2w}_to_${mpr}_t4 |
|
Compute EPI brain mask |
gauss_4dfp, imgmax_4dfp, img2msk_4dfp, maskimg_4dfp |
f_half = .3 threshold = .2 * max(blurred epi) |
${epi}_msk |
Compute EPI (iteratively) to T2w transform |
w/ original epi (source_msk = none) modes[1] = 1024 + 3 w/ masked epi (source_msk=${epi}_msk) modes[2] = 1024 + 3 modes[3] = 3072 + 3 + 8 modes[4] = 8192 + 2048 + 3 + 8 |
${epi}_to_${t2w}_t4 |
|
Combine transforms |
${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 |
${t2w}_to_${target}_t4 ${epi}_to_${target}_t4 ${epi}_to_${mpr}_t4 |
N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3
N.B.: All named images must be in 4dfp format
N.B.: -S specifies the atlas space. The only currently supported atlas space is 711-2B
epi2t2w2mpr2atl2_4dfp
EPI \(\rightarrow\) T2W \(\rightarrow\) T1W \(\rightarrow\) atlas (6 parameter cross-modal; best for distorted fMRI)
Usage: epi2t2w2mpr2atl2_4dfp <epi_anat> <t2w_anat> <mpr_anat> [useold] [711-2? OR -T<Target including path>] [-S<atlas space>]
Examples:
epi2t2w2mpr2atl2_4dfp stem9_anat_ave stem9_643-2 stem9_654-3 711-2B
epi2t2w2mpr2atl2_4dfp stem9_anat_ave stem9_654-3 useold -T/data/cninds01/atlas/NP765 -S711-2B
Processing steps
Step description |
Function |
Inputs |
Output |
|---|---|---|---|
Compute MPR to atlas transform |
mpr2atl_4dfp |
${mpr}_to_${target}_t4 |
|
Compute T2w to MPR transform |
modes[1] = 4096 + 3 modes[2] = 1024 + 3 modes[3] = 2048 + 3 modes[4] = 2048 + 3 [+ 8 + 64 if thin t2w] modes[5] = modes[4] + 8192 |
${t2w}_to_${mpr}_t4 |
|
Compute EPI brain mask |
gauss_4dfp, imgmax_4dfp, img2msk_4dfp, maskimg_4dfp |
f_half = .3 threshold = .2 * max(blurred epi) |
${epi}_msk |
Compute (iteratively) EPI to T2w transform |
w/ original epi (source_msk = none) modes[1] = 4096 + 3 modes[2] = 1024 + 3 w/ masked epi (source_msk = ${epi}_msk) modes[3] = 1024 + 3 modes[4] = 3072 + 3 modes[5] = 8192 + 2048 + 3 |
${epi}_to_${t2w}_t4 |
|
Combine transforms |
${t2w}_to_${mpr}_t4, ${mpr}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${target}_t4 ${epi}_to_${t2w}_t4, ${t2w}_to_${mpr}_t4 |
${t2w}_to_${target}_t4 ${epi}_to_${target}_t4 ${epi}_to_${mpr}_t4 |
N.B.: Any image argument may include a path, e.g., /data/petmr1/data7/stem/96_06_14_stem9/stem9_654-3
N.B.: All named images must be in 4dfp format
N.B.: -S specifies the atlas space. The only currently supported atlas space is 711-2B
cross_day_imgreg_4dfp
link first session atlas transform to subsequent sessions via EPI “anat_ave”
Usage: cross_day_imgreg_4dfp <curr_patid> <day1_atlas_path> <day1_patid> <atlas_representative_target> [options]
Examples:
cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 711-2Y
cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 -T/data/cninds01/data2/ATLAS/ALLEGRA_Y_111
Options
-a<str> |
specify image filename trailer (default = “anat_ave”) |
-nostretch |
disable stretch in transform |
-setecho |
set echo |
-S<str> |
specify atlas space (default=711-2B) |
N.B.: cross_day_imgreg_4dfp must be run in the current atlas directory
N.B.: <atlas_representative_target> may be of form 711-2? OR -T/path/image
compute_run_sd1.csh
run var_4dfp -sn4 on all bold directories (*xr3d_norm and *xr3d_atl) and makes movies
Usage: compute_run_sd1.csh <patid>
Examples:
compute_run_sd1.csh VB15792
cross_day_imgreg_4dfp
compute cross-session BOLD atlas transform
Usage: cross_day_imgreg_4dfp <curr_patid> <day1_atlas_path> <day1_patid> <atlas_representative_target> [options]
Examples:
cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 711-2Y
cross_day_imgreg_4dfp tpj0202 /data/petsun24/data1/tpj0201/atlas tpj0201 -T/data/cninds01/data2/ATLAS/ALLEGRA_Y_111
Options
-a<str> |
specify image filename trailer (default = “anat_ave”) |
-nostretch |
disable stretch in transform |
-setecho |
set echo |
-S<str> |
specify atlas space (default=711-2B) |
N.B.: cross_day_imgreg_4dfp must be run in the current atlas directory
N.B.: <atlas_representative_target> may be of form 711-2? OR -T/path/image
run_dvar_4dfp
compute format (identify frames with too much motion) (dvar_4dfp wrapper)
Usage: run_dvar_4dfp <(conc) concfile> [options]
Options
-d |
debug mode |
-v |
verbose mode |
-p<str> |
specify printer on which to plot generated .dat.ps file |
-P<str> |
print previously generated results on specified printer (run on SunOS) |
-x<flt> |
set frame rejection threshold (default = mode + 2.5*(left s.d.) over non-skipped frames) |
N.B.: run_dvar_4dfp is a wrapper for dvar_4dfp
N.B.: options -b -m -n -t are passed to dvar_4dfp
N.B.: option -s is always passed to dvar_4dfp
conc_4dfp
create conc file
Usage: conc_4dfp <(conc) outroot> <(4dfp) 1> <(4dfp) 2> …
Examples:
conc_4dfp vb13157_faln_dbnd_xr3d_atl vb13157_b?_faln_dbnd_xr3d_atl.4dfp.img
Options
-w |
supress inclusion of current working directory in listed file path |
-l<str> |
read input 4dfp list |
N.B.: output conc file always has extension “conc”
N.B.: only files in or below the current working directory can be correctly addressed
conc_mv
update conc file 4dfp image pointers
Usage: conc_mv <conc file> <from> <to>
Examples:
conc_mv TC26851_rmsp_faln_dbnd_xr3d_atl.conc /data/nil-bluearc/raichle/gusnard/np751 auto_evolve/AVI_TEST
Options
-v |
verbose mode |
-t |
practice mode (<conc file> not changed) |
conc2format
compute conc-specific format using a fixed number of pre-steady state frames
Examples:
conc2format vb13157_faln_dbnd_xr3d_atl.conc 4
Options
-v |
verbose mode |
-X |
label first frame of each run ‘X’ |
RFX2.csh
random effects analysis (1 or 2 groups)
Usage: RFX2.csh <list_group1> <Nimage_group1> [<list_group2> <Nimage_group2>]
Options
-d |
debug mode |
-R |
suppress creation of large rec files (bootstrap mode) |
N.B.: <list_group[12]> name 4dfp images on which to run the t-test
N.B.: <Nimage_group[12]> are 4dfp ‘n’ images (number of subjects for which each voxel is defined)
N.B.: If one group is entered a t-test will be run on this group against the null hypothesis of 0
N.B.: If two groups are entered a t-test will be run comparing the two groups and the computed statistic is Welch’s approximate t’ (Eqn. 8.11, p. 129 in Zar.)