where the options are
-quiet Turn off the verbose progress messages
-orient code Sets the orientation of the 3D volume(s) in the .BRIK.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
** WARNING: when changing the orientation, you must be sure
to check the origins as well, to make sure that the volume
is positioned correctly in space.
-xorigin distx Puts the center of the edge voxel off at the given
-yorigin disty distance, for the given axis (x,y,z); distances in mm.
-zorigin distz (x=first axis, y=second axis, z=third axis).
Usually, only -zorigin makes sense. Note that this
distance is in the direction given by the corresponding
letter in the -orient code. For example, '-orient RAI'
would mean that '-zorigin 30' sets the center of the
first slice at 30 mm Inferior. See the to3d manual
for more explanations of axes origins.
** SPECIAL CASE: you can use the string 'cen' in place of
a distance to force that axis to be re-centered.
-xorigin_raw xx Puts the center of the edge voxel at the given COORDINATE
-yorigin_raw yy rather than the given DISTANCE. That is, these values
-zorigin_raw zz directly replace the offsets in the dataset header,
without any possible sign changes.
-duporigin cset Copies the xorigin, yorigin, and zorigin values from
the header of dataset 'cset'.
-dxorigin dx Adds distance 'dx' (or 'dy', or 'dz') to the center
-dyorigin dy coordinate of the edge voxel. Can be used with the
-dzorigin dz values input to the 'Nudge xyz' plugin.
** WARNING: you can't use these options at the same
time you use -orient.
** WARNING: consider -shift_tags if dataset has tags
-xdel dimx Makes the size of the voxel the given dimension,
-ydel dimy for the given axis (x,y,z); dimensions in mm.
-zdel dimz ** WARNING: if you change a voxel dimension, you will
probably have to change the origin as well.
-keepcen When changing a voxel dimension with -xdel (etc.),
also change the corresponding origin to keep the
center of the dataset at the same coordinate location.
-xyzscale fac Scale the size of the dataset voxels by the factor 'fac'.
This is equivalent to using -xdel, -ydel, -zdel together.
-keepcen is used on the first input dataset, and then
any others will be shifted the same amount, to maintain
their alignment with the first one.
** WARNING: -xyzscale can't be used with any of the other
options that change the dataset grid coordinates!
** N.B.: 'fac' must be positive, and using fac=1.0 is stupid.
-TR time Changes the TR time to a new value (see 'to3d -help').
** You can also put the name of a dataset in for 'time', in
which case the TR for that dataset will be used.
** N.B.: If the dataset has slice time offsets, these will
be scaled by the factor newTR/oldTR. This scaling does not
apply if you use '-Tslices' in the same 3drefit run.
-notoff Removes the slice-dependent time-offsets.
-Torg ttt Set the time origin of the dataset to value 'ttt'.
(Time origins are set to 0 in to3d.)
** WARNING: These 3 options apply only to 3D+time datasets.
**N.B.: Using '-TR' on a dataset without a time axis
will add a time axis to the dataset.
-Tslices a b c d ...
Reset the slice time offsets to be 'a', 'b', 'c', ...
(in seconds). The number of values following '-Tslices'
should be the same as the number of slices in the dataset,
but 3drefit does NOT check that this is true.
** If any offset time is < 0 or >= TR, a warning will be
printed (to stderr), but this is not illegal even though
it is a bad idea.
** If the dataset does not have a TR set, then '-Tslices'
will fail. You can use '-TR' to set the inter-volume time
spacing in the same 3drefit command.
** If you have the slices times stored (e.g., from DICOM) in
some other units, you can scale them to be in seconds by
putting a scale factor after the '-Tslices' option as follows:
-Tslices '*0.001' 300 600 900 ...
which would be used to scale from milliseconds to seconds.
The format is to start the scale factor with a '*' to tell
3drefit that this number is not a slice offset but is to be
used a a scale factor for the rest of the following values.
Since '*' is a filename wildcard, it needs to be in quotes!
** The program stops looking for number values after '-Tslices'
when it runs into something that does not look like a number.
Here, 'look like a number' means a character string that:
* starts with a digit 0..9
* starts with a decimal point '.' followed by a digit
* starts with a minus sign '-' followed by a digit
* starts with '-.' followed by a digit
So if the input dataset name starts with a digit, and the
last command line option '-Tslices', 3drefit will think
the filename is actually a number for a slice offset time.
To avoid this problem, you can do one of these things:
* Put in an option that is just the single character '-'
* Don't use '-Tslices' as the last option
* Put a directory name before the dataset name, as in
'./Galacticon.nii'
** If you have the slice time offsets stored in a text file
as a list of values, then you can input these values on
the command line using the Unix backquote operator, as in
-Tslices `cat SliceTimes.1D`
** For example, if the slice time offsets are in a JSON
sidecar (a la BIDS), you might be able to something like
the following to extract the timings into a file:
abids_json_tool.py -json2txt -input sub-10506_task-pamenc_bold.json -prefix junk.txt
grep SliceTiming junk.txt | sed -e 's/^SliceTiming *://' > SliceTimes.1D
\rm junk.txt
-newid Changes the ID code of this dataset as well.
-nowarp Removes all warping information from dataset.
-apar aset Set the dataset's anatomy parent dataset to 'aset'
** N.B.: The anatomy parent is the dataset from which the
transformation from +orig to +acpc and +tlrc coordinates
is taken. It is appropriate to use -apar when there is
more than 1 anatomical dataset in a directory that has
been transformed. In this way, you can be sure that
AFNI will choose the correct transformation. You would
use this option on all the +orig dataset that are
aligned with 'aset' (i.e., that were acquired in the
same scanning session).
** N.B.: Special cases of 'aset'
aset = NULL --> remove the anat parent info from the dataset
aset = SELF --> set the anat parent to be the dataset itself
-wpar wset Set the warp parent (the +orig version of a +tlrc dset).
This option is used by @auto_tlrc. Do not use it unless
you know what you're doing.
-clear_bstat Clears the statistics (min and max) stored for each sub-brick
in the dataset. This is useful if you have done something to
modify the contents of the .BRIK file associated with this
dataset.
-redo_bstat Re-computes the statistics for each sub-brick. Requires
reading the .BRIK file, of course. Also does -clear_bstat
before recomputing statistics, so that if the .BRIK read
fails for some reason, then you'll be left without stats.
-statpar v ... Changes the statistical parameters stored in this
dataset. See 'to3d -help' for more details.
-markers Adds an empty set of AC-PC markers to the dataset,
if it can handle them (is anatomical, is in the +orig
view, and isn't 3D+time).
** WARNING: this will erase any markers that already exist!
-shift_tags Apply -dxorigin (and y and z) changes to tags.
-dxtag dx Add dx to the coordinates of all tags.
-dytag dy Add dy to the coordinates of all tags.
-dztag dz Add dz to the coordinates of all tags.
-view code Changes the 'view' to be 'code', where the string 'code'
is one of 'orig', 'acpc', or 'tlrc'.
** WARNING: The program will also change the .HEAD and .BRIK
filenames to match. If the dataset filenames already
exist in the '+code' view, then this option will fail.
You will have to rename the dataset files before trying
to use '-view'. If you COPY the files and then use
'-view', don't forget to use '-newid' as well!
** WARNING2: Changing the view without specifying the new
might lead to conflicting information. Consider specifying
the space along with -view
-space spcname Associates the dataset with a specific template type, e.g.
TLRC, MNI, ORIG. The default assumed for +tlrc datasets is
'TLRC'. One use for this attribute is to use MNI space
coordinates and atlases instead of the default TLRC space.
** See WARNING2 for -view option.
-cmap cmaptype Associate colormap type with dataset. Available choices are
CONT_CMAP (the default), INT_CMAP (integer colormap display)
and SPARSE_CMAP (for sparse integer colormaps). INT_CMAP is
appropriate for showing ROI mask datasets or Atlas datasets
where the continuous color scales are not useful.
-label2 llll Set the 'label2' field in a dataset .HEAD file to the
string 'llll'. (Can be used as in AFNI window titlebars.)
-labeltable TTT Inset the label table TTT in the .HEAD file.
The label table format is described in README.environment
under the heading: 'Variable: AFNI_VALUE_LABEL_DTABLE'
See also -copytables
-denote Means to remove all possibly-identifying notes from
the header. This includes the History Note, other text
Notes, keywords, and labels.
-deoblique Replace transformation matrix in header with cardinal matrix.
This option DOES NOT deoblique the volume. To do so
you should use 3dWarp -deoblique. This option is not
to be used unless you really know what you're doing.
-oblique_origin
assume origin and orientation from oblique transformation
matrix rather than traditional cardinal information
-oblique_recenter
Adjust the origin so that the cardinalized 0,0,0 is in
the same brain location as that of the original (oblique?)
(scanner?) coordinates.
Round this to the nearest voxel center.
* Even if cardinal, rounding might cause an origin shift
(see -oblique_recenter_raw).
-oblique_recenter_raw
Like -oblique_recenter, but do not round.
So coordinate 0,0,0 is in the exact same location, even
if not at a voxel center.
-byteorder bbb Sets the byte order string in the header.
Allowable values for 'bbb' are:
LSB_FIRST MSB_FIRST NATIVE_ORDER
Note that this does not change the .BRIK file!
This is done by programs 2swap and 4swap.
-checkaxes Doesn't alter the input dataset; rather, this just
checks the dataset axes orientation codes and the
axes matrices for consistency. (This option was
added primarily to check for bugs in various codes.)
-appkey ll Appends the string 'll' to the keyword list for the
whole dataset.
-repkey ll Replaces the keyword list for the dataset with the
string 'll'.
-empkey Destroys the keyword list for the dataset.
-atrcopy dd nn Copy AFNI header attribute named 'nn' from dataset 'dd'
into the header of the dataset(s) being modified.
For more information on AFNI header attributes, see
documentation file README.attributes. More than one
'-atrcopy' option can be used.
**N.B.: This option is for those who know what they are doing!
Without the -saveatr option, this option is
meant to be used to alter attributes that are NOT
directly mapped into dataset internal structures, since
those structures are mapped back into attribute values
as the dataset is being written to disk. If you want
to change such an attribute, you have to use the
corresponding 3drefit option directly or use the
-saveatr option.
If you are confused, try to understand this:
Option -atrcopy was never intended to modify AFNI-
specific attributes. Rather, it was meant to copy
user-specific attributes that had been added to some
dataset using -atrstring option. A cursed day came when
it was convenient to use -atrcopy to copy an AFNI-specific
attribute (BRICK_LABS to be exact) and for that to
take effect in the output, the option -saveatr was added.
Contact Daniel Glen and/or Rick Reynolds for further
clarification and any other needs you may have.
Do NOT use -atrcopy or -atrstring with other modification
options.
See also -copyaux
-atrstring n 'x' Copy the string 'x' into the dataset(s) being
modified, giving it the attribute name 'n'.
To be safe, the 'x' string should be in quotes.
**N.B.: You can store attributes with almost any name in
the .HEAD file. AFNI will ignore those it doesn't
know anything about. This technique can be a way of
communicating information between programs. However,
when most AFNI programs write a new dataset, they will
not preserve any such non-standard attributes.
**N.B.: Special case: if the string 'x' is of the form
'file:name', then the contents of the file 'name' will
be read in as a single string and stored in the attribute.
-atrfloat name 'values'
-atrint name 'values'
Create or modify floating point or integer attributes.
The input values may be specified as a single string
in quotes or as a 1D filename or string. For example,
3drefit -atrfloat IJK_TO_DICOM_REAL '1 0.2 0 0 -0.2 1 0 0 0 0 1 0' dset+orig
3drefit -atrfloat IJK_TO_DICOM_REAL flipZ.1D dset+orig
3drefit -atrfloat IJK_TO_DICOM_REAL \
'1D:1,0.2,2@0,-0.2,1,2@0,2@0,1,0' \
dset+orig
Almost all afni attributes can be modified in this way
-saveatr (default) Copy the attributes that are known to AFNI into
the dset->dblk structure thereby forcing changes to known
attributes to be present in the output.
This option only makes sense with -atrcopy
**N.B.: Don't do something like copy labels of a dataset with
30 sub-bricks to one that has only 10, or vice versa.
This option is for those who would deservedly earn a
hunting license.
-nosaveatr Opposite of -saveatr
Example:
3drefit -saveatr -atrcopy WithLabels+tlrc BRICK_LABS NeedsLabels+tlrc
-'type' Changes the type of data that is declared for this
dataset, where 'type' is chosen from the following:
ANATOMICAL TYPES
spgr == Spoiled GRASS fse == Fast Spin Echo
epan == Echo Planar anat == MRI Anatomy
ct == CT Scan spct == SPECT Anatomy
pet == PET Anatomy mra == MR Angiography
bmap == B-field Map diff == Diffusion Map
omri == Other MRI abuc == Anat Bucket
FUNCTIONAL TYPES
fim == Intensity fith == Inten+Thr
fico == Inten+Cor fitt == Inten+Ttest
fift == Inten+Ftest fizt == Inten+Ztest
fict == Inten+ChiSq fibt == Inten+Beta
fibn == Inten+Binom figt == Inten+Gamma
fipt == Inten+Poisson fbuc == Func-Bucket
-copyaux auxset Copies the 'auxiliary' data from dataset 'auxset'
over the auxiliary data for the dataset being
modified. Auxiliary data comprises sub-brick labels,
keywords, statistics codes, nodelists, and labeltables
AND/OR atlas point lists.
'-copyaux' occurs BEFORE the '-sub' operations below,
so you can use those to alter the auxiliary data
that is copied from auxset.
-copytables tabset Copies labeltables AND/OR atlas point lists, if any,
from tabset to the input dataset.
'-copyaux' occurs BEFORE the '-sub' operations below,
so you can use those to alter the auxiliary data
that is copied from tabset.
-relabel_all xx Reads the file 'xx', breaks it into strings,
and puts these strings in as the sub-brick
labels. Basically a batch way of doing
'-sublabel' many times, for n=0, 1, ...
** This option is executed BEFORE '-sublabel',
so any labels from '-sublabel' will over-ride
labels from this file.
** Strings in the 'xx' file are separated by
whitespace (blanks, tabs, new lines).
-relabel_all_str 'lab0 lab1 ... lab_p': Just like -relabel_all
but with labels all present in one string
-sublabel_prefix PP: Prefix each sub-brick's label with PP
-sublabel_suffix SS: Suffix each sub-brick's label with SS
