running rapidtide with no arguments gives usage string twice
Closed this issue · 0 comments
dmd commented
(I have only tested this through Docker.)
Observe below - note that the "usage:" line happens twice.
$ docker run -it fredericklab/rapidtide rapidtide
/usr/local/miniconda/lib/python3.9/site-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.8) or chardet (5.0.0)/charset_normalizer (2.0.4) doesn't match a supported version!
warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
mklexists: False
usage: rapidtide
[-h]
[--denoising | --delaymapping]
[--venousrefine | --nirs]
[--datatstep TSTEP | --datafreq FREQ]
[--noantialias]
[--invert]
[--interptype {univariate,cubic,quadratic}]
[--offsettime OFFSETTIME]
[--autosync]
[--filterband {None,vlf,lfo,resp,cardiac,lfo_legacy}]
[--filterfreqs LOWERPASS UPPERPASS]
[--filterstopfreqs LOWERSTOP UPPERSTOP]
[--filtertype {trapezoidal,brickwall,butterworth}]
[--butterorder ORDER]
[--padseconds SECONDS]
[--permutationmethod {shuffle,phaserandom}]
[--numnull NREPS]
[--skipsighistfit]
[--windowfunc {hamming,hann,blackmanharris,None}]
[--nowindow]
[--zeropadding PADVAL]
[--detrendorder ORDER]
[--spatialfilt GAUSSSIGMA]
[--globalmean]
[--globalmaskmethod {mean,variance}]
[--globalpreselect]
[--globalmeaninclude MASK[:VALSPEC]]
[--globalmeanexclude MASK[:VALSPEC]]
[--motionfile MOTFILE]
[--motpos]
[--motderiv]
[--motdelayderiv]
[--globalsignalmethod {sum,meanscale,pca}]
[--globalpcacomponents VALUE]
[--slicetimes FILE]
[--numskip SKIP]
[--timerange START END]
[--nothresh]
[--oversampfac OVERSAMPFAC]
[--regressor FILE]
[--regressorfreq FREQ | --regressortstep TSTEP]
[--regressorstart START]
[--corrweighting {None,phat,liang,eckart}]
[--corrtype {linear,circular}]
[--corrmaskthresh PCT | --corrmask MASK[:VALSPEC]]
[--similaritymetric {correlation,mutualinfo,hybrid}]
[--mutualinfosmoothingtime TAU]
[--fixdelay DELAYTIME | --searchrange LAGMIN LAGMAX]
[--sigmalimit SIGMALIMIT]
[--bipolar]
[--nofitfilt]
[--peakfittype {gauss,fastgauss,quad,fastquad,COM,None}]
[--despecklepasses PASSES]
[--despecklethresh VAL]
[--refineprenorm {None,mean,var,std,invlag}]
[--refineweighting {None,NIRS,R,R2}]
[--passes PASSES]
[--refineinclude MASK[:VALSPEC]]
[--refineexclude MASK[:VALSPEC]]
[--norefinedespeckled]
[--lagminthresh MIN]
[--lagmaxthresh MAX]
[--ampthresh AMP]
[--sigmathresh SIGMA]
[--norefineoffset]
[--psdfilter]
[--pickleft]
[--pickleftthresh THRESH]
[--refineupperlag | --refinelowerlag]
[--refinetype {pca,ica,weighted_average,unweighted_average}]
[--pcacomponents VALUE]
[--convergencethresh THRESH]
[--maxpasses MAXPASSES]
[--nolimitoutput]
[--savelags]
[--histlen HISTLEN]
[--glmsourcefile FILE]
[--noglm]
[--preservefiltering]
[--saveintermediatemaps]
[--legacyoutput]
[--calccoherence]
[--noprogressbar]
[--checkpoint]
[--wiener]
[--spcalculation]
[--dpoutput]
[--cifti]
[--simulate]
[--displayplots]
[--nonumba]
[--nosharedmem]
[--memprofile]
[--mklthreads MKLTHREADS]
[--nprocs NPROCS]
[--version]
[--echocancel]
[--respdelete]
[--negativegradient]
[--cleanrefined]
[--dispersioncalc]
[--acfix]
[--tmask FILE]
[--debug]
[--verbose]
[--alwaysmultiproc]
[--singleproc_getNullDist]
[--singleproc_calcsimilarity]
[--singleproc_peakeval]
[--singleproc_fitcorr]
[--singleproc_glm]
in_file
outputname
rapidtide: error: the following arguments are required: in_file, outputname
usage: rapidtide
[-h]
[--denoising | --delaymapping]
[--venousrefine | --nirs]
[--datatstep TSTEP | --datafreq FREQ]
[--noantialias]
[--invert]
[--interptype {univariate,cubic,quadratic}]
[--offsettime OFFSETTIME]
[--autosync]
[--filterband {None,vlf,lfo,resp,cardiac,lfo_legacy}]
[--filterfreqs LOWERPASS UPPERPASS]
[--filterstopfreqs LOWERSTOP UPPERSTOP]
[--filtertype {trapezoidal,brickwall,butterworth}]
[--butterorder ORDER]
[--padseconds SECONDS]
[--permutationmethod {shuffle,phaserandom}]
[--numnull NREPS]
[--skipsighistfit]
[--windowfunc {hamming,hann,blackmanharris,None}]
[--nowindow]
[--zeropadding PADVAL]
[--detrendorder ORDER]
[--spatialfilt GAUSSSIGMA]
[--globalmean]
[--globalmaskmethod {mean,variance}]
[--globalpreselect]
[--globalmeaninclude MASK[:VALSPEC]]
[--globalmeanexclude MASK[:VALSPEC]]
[--motionfile MOTFILE]
[--motpos]
[--motderiv]
[--motdelayderiv]
[--globalsignalmethod {sum,meanscale,pca}]
[--globalpcacomponents VALUE]
[--slicetimes FILE]
[--numskip SKIP]
[--timerange START END]
[--nothresh]
[--oversampfac OVERSAMPFAC]
[--regressor FILE]
[--regressorfreq FREQ | --regressortstep TSTEP]
[--regressorstart START]
[--corrweighting {None,phat,liang,eckart}]
[--corrtype {linear,circular}]
[--corrmaskthresh PCT | --corrmask MASK[:VALSPEC]]
[--similaritymetric {correlation,mutualinfo,hybrid}]
[--mutualinfosmoothingtime TAU]
[--fixdelay DELAYTIME | --searchrange LAGMIN LAGMAX]
[--sigmalimit SIGMALIMIT]
[--bipolar]
[--nofitfilt]
[--peakfittype {gauss,fastgauss,quad,fastquad,COM,None}]
[--despecklepasses PASSES]
[--despecklethresh VAL]
[--refineprenorm {None,mean,var,std,invlag}]
[--refineweighting {None,NIRS,R,R2}]
[--passes PASSES]
[--refineinclude MASK[:VALSPEC]]
[--refineexclude MASK[:VALSPEC]]
[--norefinedespeckled]
[--lagminthresh MIN]
[--lagmaxthresh MAX]
[--ampthresh AMP]
[--sigmathresh SIGMA]
[--norefineoffset]
[--psdfilter]
[--pickleft]
[--pickleftthresh THRESH]
[--refineupperlag | --refinelowerlag]
[--refinetype {pca,ica,weighted_average,unweighted_average}]
[--pcacomponents VALUE]
[--convergencethresh THRESH]
[--maxpasses MAXPASSES]
[--nolimitoutput]
[--savelags]
[--histlen HISTLEN]
[--glmsourcefile FILE]
[--noglm]
[--preservefiltering]
[--saveintermediatemaps]
[--legacyoutput]
[--calccoherence]
[--noprogressbar]
[--checkpoint]
[--wiener]
[--spcalculation]
[--dpoutput]
[--cifti]
[--simulate]
[--displayplots]
[--nonumba]
[--nosharedmem]
[--memprofile]
[--mklthreads MKLTHREADS]
[--nprocs NPROCS]
[--version]
[--echocancel]
[--respdelete]
[--negativegradient]
[--cleanrefined]
[--dispersioncalc]
[--acfix]
[--tmask FILE]
[--debug]
[--verbose]
[--alwaysmultiproc]
[--singleproc_getNullDist]
[--singleproc_calcsimilarity]
[--singleproc_peakeval]
[--singleproc_fitcorr]
[--singleproc_glm]
in_file
outputname
Perform a
RIPTiDe
time delay
analysis on
a dataset.
positional arguments:
in_file
The input
data file
(BOLD fMRI
file or
NIRS text
file).
outputname
The root
name for
the output
files. For
BIDS
compliance,
this can
only
contain
valid BIDS
entities
from the
source
data.
optional arguments:
-h, --help
show this
help
message and
exit
--permutationmethod {shuffle,phaserandom}
Permutation
method for
significanc
e testing.
Default is
"shuffle".
--numnull NREPS
Estimate si
gnificance
threshold
by running
NREPS null
correlation
s (default
is 10000,
set to 0 to
disable).
--skipsighistfit
Do not fit
significanc
e histogram
with a
Johnson SB
function.
Analysis type:
Single
arguments
that
change
default
values
for many
arguments
. Any
parameter
set by an
analysis
type can
be overri
dden by
setting
that
parameter
explicitl
y.
Analysis
types are
mutually
exclusive
with one
another.
--denoising
Preset for
hemodynamic
denoising -
this is a
macro that
sets lagmin
=-10.0, lag
max=10.0,
passes=3, d
especkle_pa
sses=4, ref
ineoffset=T
rue, peakfi
ttype=gauss
, doglmfilt
=True. Any
of these
options can
be
overridden
with the
appropriate
additional
arguments.
--delaymapping
Preset for
delay
mapping
analysis -
this is a
macro that
sets lagmin
=-10.0, lag
max=30.0,
passes=3, d
especkle_pa
sses=4, ref
ineoffset=T
rue, pickle
ft=True, li
mitoutput=T
rue, doglmf
ilt=False.
Any of
these
options can
be
overridden
with the
appropriate
additional
arguments.
Macros:
Single
arguments
that
change
default
values
for many
arguments
. Macros
override
individua
lly set p
arameters
. Macros
are
mutually
exclusive
with one
another.
--venousrefine
This is a
macro that
sets --lagm
inthresh=2.
5, --lagmax
thresh=6.0,
--ampthresh
=0.5, and -
-refineuppe
rlag to
bias
refinement
towards
voxels in
the
draining
vasculature
for an fMRI
scan.
--nirs
This is a
NIRS
analysis -
this is a
macro that
sets
--nothresh,
--refinepre
norm=var, -
-ampthresh=
0.7, and --
lagminthres
h=0.1.
Preprocessing options:
--datatstep TSTEP
Set the
timestep of
the data
file to
TSTEP. This
will
override
the TR in
an fMRI
file. NOTE:
if using
data from a
text file,
for example
with NIRS
data, using
one of
these
options is
mandatory.
--datafreq FREQ
Set the
timestep of
the data
file to
1/FREQ.
This will
override
the TR in
an fMRI
file. NOTE:
if using
data from a
text file,
for example
with NIRS
data, using
one of
these
options is
mandatory.
--noantialias
Disable ant
ialiasing
filter.
--invert
Invert the
sign of the
regressor
before
processing.
--interptype {univariate,cubic,quadratic}
Use
specified i
nterpolatio
n type.
Options are
"cubic", "q
uadratic",
and "univar
iate".
Default is
univariate.
--offsettime OFFSETTIME
Apply
offset
OFFSETTIME
to the lag
regressors.
--autosync
Estimate
and apply
the initial
offsettime
of an
external
regressor
using the
global cros
scorrelatio
n.
Overrides
offsettime
if present.
--detrendorder ORDER
Set order
of trend
removal (0
to
disable).
Default is
3.
--spatialfilt GAUSSSIGMA
Spatially
filter fMRI
data prior
to analysis
using
GAUSSSIGMA
in mm. Set
GAUSSSIGMA
negative to
have
rapidtide
set it to
half the
mean voxel
dimension
(a rule of
thumb for a
good
value).
--globalmean
Generate a
global mean
regressor
and use
that as the
reference
regressor.
If no
external
regressor
is
specified,
this is
enabled by
default.
--globalmaskmethod {mean,variance}
Select
whether to
use
timecourse
mean or
variance to
mask voxels
prior to
generating
global
mean.
Default is
"mean".
--globalpreselect
Treat this
run as an
initial
pass to
locate good
candidate
voxels for
global mean
regressor
generation.
--globalmeaninclude MASK[:VALSPEC]
Only use
voxels in
mask file
NAME for
global
regressor
generation
(if VALSPEC
is given,
only voxels
with
integral
values
listed in
VALSPEC are
used).
--globalmeanexclude MASK[:VALSPEC]
Do not use
voxels in
mask file
NAME for
global
regressor
generation
(if VALSPEC
is given,
only voxels
with
integral
values
listed in
VALSPEC are
excluded).
--motionfile MOTFILE
Read 6
columns of
motion
regressors
out of
MOTFILE
file (.par
or BIDS
.json)
(with
timepoints
rows) and
regress
their
derivatives
and delayed
derivatives
out of the
data prior
to
analysis.
--motpos
Toggle
whether dis
placement
regressors
will be
used in
motion
regression.
Default is
False.
--motderiv
Toggle
whether
derivatives
will be
used in
motion
regression.
Default is
True.
--motdelayderiv
Toggle
whether
delayed
derivative
regressors
will be
used in
motion
regression.
Default is
False.
--globalsignalmethod {sum,meanscale,pca}
The method
for constru
cting the
initial
global
signal
regressor -
straight
summation,
mean
scaling
each voxel
prior to
summation,
or MLE PCA
of the
voxels in
the global
signal
mask.
Default is
"sum."
--globalpcacomponents VALUE
Number of
PCA
components
used for
estimating
the global
signal. If
VALUE >= 1,
will retain
thismany
components.
If 0.0 <
VALUE <
1.0, enough
components
will be
retained to
explain the
fraction
VALUE of
the total
variance.
If VALUE is
negative,
the number
of
components
will be to
retain will
be selected
automatical
ly using
the MLE
method.
Default is
0.8.
--slicetimes FILE
Apply
offset
times from
FILE to
each slice
in the
dataset.
--numskip SKIP
SKIP TRs
were
previously
deleted
during prep
rocessing
(e.g. if
you have
done your p
reprocessin
g in FSL
and set
dummypoints
to a
nonzero
value.)
Default is
0.
--timerange START END
Limit
analysis to
data
between
timepoints
START and
END in the
fmri file.
If END is
set to -1,
analysis
will go to
the last
timepoint.
Negative
values of
START will
be set to
0. Default
is to use
all
timepoints.
--nothresh
Disable
voxel
intensity
threshold
(especially
useful for
NIRS data).
Filtering options:
--filterband {None,vlf,lfo,resp,cardiac,lfo_legacy}
Filter data
and
regressors
to specific
band. Use
"None" to
disable
filtering.
Default is
"lfo".
--filterfreqs LOWERPASS UPPERPASS
Filter data
and
regressors
to retain
LOWERPASS
to
UPPERPASS.
If --filter
stopfreqs
is not also
specified,
LOWERSTOP
and
UPPERSTOP
will be
calculated
automatical
ly.
--filterstopfreqs LOWERSTOP UPPERSTOP
Filter data
and
regressors
to with
stop
frequencies
LOWERSTOP
and
UPPERSTOP.
LOWERSTOP
must be <=
LOWERPASS,
UPPERSTOP
must be >=
UPPERPASS.
Using this
argument
requires
the use of
--filterfre
qs.
--filtertype {trapezoidal,brickwall,butterworth}
Filter data
and
regressors
using a
trapezoidal
FFT,
brickwall
FFT, or
butterworth
bandpass
filter.
Default is
"trapezoida
l".
--butterorder ORDER
Set order
of
butterworth
filter (if
used).
Default is
6.
--padseconds SECONDS
The number
of seconds
of padding
to add to
each end of
a filtered
timecourse
to reduce
end
effects.
Default is
30.0.
Windowing options:
--windowfunc {hamming,hann,blackmanharris,None}
Window
function to
use prior
to correlat
ion.
Options are
hamming,
hann, black
manharris,
and None.
Default is
hamming
--nowindow
Disable pre
correlation
windowing.
--zeropadding PADVAL
Pad input
functions
to
correlation
with PADVAL
zeros on
each side.
A PADVAL of
0 does
circular co
rrelations,
positive
values
reduce edge
artifacts.
Set PADVAL
< 0 to set
automatical
ly. Default
is 0.
Correlation options:
--oversampfac OVERSAMPFAC
Oversample
the fMRI
data by the
following
integral
factor. Set
to -1 for
automatic
selection
(default).
--regressor FILE
Read the
initial
probe
regressor
from file
FILE (if
not
specified,
generate
and use the
global
regressor).
--regressorfreq FREQ
Probe
regressor
in file has
sample
frequency
FREQ
(default is
1/tr) NB: -
-regressorf
req and --r
egressortst
ep) are two
ways to
specify the
same thing.
--regressortstep TSTEP
Probe
regressor
in file has
sample
frequency
FREQ
(default is
1/tr) NB: -
-regressorf
req and --r
egressortst
ep) are two
ways to
specify the
same thing.
--regressorstart START
The time
delay in
seconds
into the
regressor
file, corre
sponding in
the first
TR of the
fMRI file
(default is
0.0).
--corrweighting {None,phat,liang,eckart}
Method to
use for
cross-
correlation
weighting.
Default is
"None".
--corrtype {linear,circular}
Cross-
correlation
type
(linear or
circular).
Default is
"circular".
--corrmaskthresh PCT
Do correlat
ions in
voxels
where the
mean
exceeds
this
percentage
of the
robust max.
Default is
1.0.
--corrmask MASK[:VALSPEC]
Only do cor
relations
in nonzero
voxels in
NAME (if
VALSPEC is
given, only
voxels with
integral
values
listed in
VALSPEC are
used).
--similaritymetric {correlation,mutualinfo,hybrid}
Similarity
metric for
finding
delay
values.
Choices are
"correlatio
n", "mutual
info", and
"hybrid".
Default is
correlation
.
--mutualinfosmoothingtime TAU
Time
constant of
a temporal
smoothing
function to
apply to
the mutual
information
function.
Default is
3.0
seconds.
TAU <=0.0
disables
smoothing.
Correlation fitting options:
--fixdelay DELAYTIME
Don't fit
the delay
time - set
it to
DELAYTIME
seconds for
all voxels.
--searchrange LAGMIN LAGMAX
Limit fit
to a range
of lags
from LAGMIN
to LAGMAX.
Default is
-30.0 to
30.0
seconds.
--sigmalimit SIGMALIMIT
Reject lag
fits with
linewidth
wider than
SIGMALIMIT
Hz. Default
is 1000.0
Hz.
--bipolar
Bipolar
mode -
match peak
correlation
ignoring
sign.
--nofitfilt
Do not zero
out peak
fit values
if fit
fails.
--peakfittype {gauss,fastgauss,quad,fastquad,COM,None}
Method for
fitting the
peak of the
similarity
function
"gauss"
performs a
Gaussian
fit, and is
most
accurate.
"quad" and
"fastquad"
use a
quadratic
fit, which
is faster,
but not as
well
tested.
Default is
"gauss".
--despecklepasses PASSES
Detect and
refit
suspect cor
relations
to disambig
uate peak
locations
in PASSES
passes.
Default is
to perform
4 passes.
Set to 0 to
disable.
--despecklethresh VAL
Refit
correlation
if median d
iscontinuit
y magnitude
exceeds
VAL.
Default is
5.0
seconds.
Regressor refinement options:
--refineprenorm {None,mean,var,std,invlag}
Apply TYPE
prenormaliz
ation to
each
timecourse
prior to
refinement.
Default is
"mean".
--refineweighting {None,NIRS,R,R2}
Apply TYPE
weighting
to each
timecourse
prior to
refinement.
Default is
"R2".
--passes PASSES
Set the
number of
processing
passes to
PASSES.
Default is
3.
--refineinclude MASK[:VALSPEC]
Only use
voxels in
file MASK
for
regressor
refinement
(if VALSPEC
is given,
only voxels
with
integral
values
listed in
VALSPEC are
used).
--refineexclude MASK[:VALSPEC]
Do not use
voxels in
file MASK
for
regressor
refinement
(if VALSPEC
is given,
voxels with
integral
values
listed in
VALSPEC are
excluded).
--norefinedespeckled
Do not use
despeckled
pixels in
calculating
the refined
regressor.
--lagminthresh MIN
For
refinement,
exclude
voxels with
delays less
than MIN.
Default is
0.5
seconds.
--lagmaxthresh MAX
For
refinement,
exclude
voxels with
delays
greater
than MAX.
Default is
5.0
seconds.
--ampthresh AMP
For
refinement,
exclude
voxels with
correlation
coefficient
s less than
AMP
(default is
0.3). NOTE:
ampthresh
will automa
tically be
set to the
p<0.05 sign
ificance
level
determined
by the
--numnull
option if
NREPS is
set greater
than 0 and
this is not
manually
specified.
--sigmathresh SIGMA
For
refinement,
exclude
voxels with
widths
greater
than SIGMA
seconds.
Default is
100.0
seconds.
--norefineoffset
Disable
realigning
refined
regressor
to zero
lag.
--psdfilter
Apply a PSD
weighted
Wiener
filter to
shifted
timecourses
prior to
refinement.
--pickleft
Will select
the
leftmost
delay peak
when
setting the
refine
offset.
--pickleftthresh THRESH
Threshhold
value
(fraction
of maximum)
in a
histogram
to be
considered
the start
of a peak.
Default is
0.33.
--refineupperlag
Only use
positive
lags for
regressor
refinement.
--refinelowerlag
Only use
negative
lags for
regressor
refinement.
--refinetype {pca,ica,weighted_average,unweighted_average}
Method with
which to
derive
refined
regressor.
Default is
"pca".
--pcacomponents VALUE
Number of
PCA
components
used for
refinement.
If VALUE >=
1, will
retain this
many
components.
If 0.0 <
VALUE <
1.0, enough
components
will be
retained to
explain the
fraction
VALUE of
the total
variance.
If VALUE is
negative,
the number
of
components
will be to
retain will
be selected
automatical
ly using
the MLE
method.
Default is
0.8.
--convergencethresh THRESH
Continue
refinement
until the
MSE between
regressors
becomes <=
THRESH. By
default,
this is not
set, so
refinement
will run
for the
specified
number of
passes.
--maxpasses MAXPASSES
Terminate
refinement
after
MAXPASSES
passes,
whether or
not
convergence
has
occured.
Default is
15.
Output options:
--nolimitoutput
Save some
of the
large and
rarely used
files.
--savelags
Save a
table of
lagtimes
used.
--histlen HISTLEN
Change the
histogram
length to
HISTLEN.
Default is
101.
--glmsourcefile FILE
Regress
delayed
regressors
out of FILE
instead of
the initial
fmri file
used to
estimate
delays.
--noglm
Turn off
GLM
filtering
to remove
delayed
regressor
from each
voxel
(disables
output of
fitNorm).
--preservefiltering
Don't
reread data
prior to
performing
GLM.
--saveintermediatemaps
Save lag
times,
strengths,
widths, and
mask for
each pass.
--legacyoutput
Use legacy
file naming
and formats
rather than
BIDS naming
and format
conventions
for output
files.
--calccoherence
Calculate
and save
the
coherence
between the
final
regressor
and the
data.
Miscellaneous options:
--noprogressbar
Will
disable
showing
progress
bars
(helpful if
stdout is
going to a
file).
--checkpoint
Enable run
checkpoints
.
--wiener
Do Wiener d
econvolutio
n to find
voxel
transfer
function.
--spcalculation
Use single
precision
for
internal ca
lculations
(may be
useful when
RAM is
limited).
--dpoutput
Use double
precision
for output
files.
--cifti
Data file
is a
converted
CIFTI.
--simulate
Simulate a
run - just
report
command
line
options.
--displayplots
Display
plots of
interesting
timecourses
.
--nonumba
Disable jit
compilation
with numba.
--nosharedmem
Disable use
of shared
memory for
large array
storage.
--memprofile
Enable
memory
profiling -
warning:
this slows
things down
a lot.
--mklthreads MKLTHREADS
Use no more
than
MKLTHREADS
worker
threads in
accelerated
numpy
calls.
--nprocs NPROCS
Use NPROCS
worker
processes
for multipr
ocessing.
Setting
NPROCS to
less than 1
sets the
number of
worker
processes
to n_cpus -
1.
--version
Print
version
information
and exit.
Experimental options (not fully tested, may not work):
--echocancel
Attempt to
perform
echo cancel
lation.
--respdelete
Attempt to
detect and
remove
respiratory
signal that
strays into
the LFO
band.
--negativegradient
Calculate
the
negative
gradient of
the fmri
data after
spectral
filtering
so you can
look for
CSF flow à
la https://
www.biorxiv
.org/conten
t/10.1101/2
021.03.29.4
37406v1.ful
l.
--cleanrefined
Perform
additional
processing
on refined
regressor
to remove
spurious
components.
--dispersioncalc
Generate
extra data
during
refinement
to allow
calculation
of
dispersion.
--acfix
Perform a
secondary
correlation
to disambig
uate peak
location. E
xperimental
.
--tmask FILE
Only
correlate
during
epochs
specified
in MASKFILE
(NB: each
line of
FILE
contains
the time
and
duration of
an epoch to
include.
Debugging options. You probably don't want to use any of these unless I ask you to to help diagnose a problem:
--debug
Enable
additional
debugging
output.
--verbose
Enable
additional
runtime
information
output.
--alwaysmultiproc
Use the mul
tiprocessin
g code path
even when
nprocs=1.
--singleproc_getNullDist
Force
single proc
path for ge
tNullDist.
--singleproc_calcsimilarity
Force
single proc
path for ca
lcsimilarit
y.
--singleproc_peakeval
Force
single proc
path for
peakeval.
--singleproc_fitcorr
Force
single proc
path for
fitcorr.
--singleproc_glm
Force
single proc
path for
glm.