mincreshape - cuts a hyperslab out of a minc file (with dimension re-
mincreshape [<options>] <infile>.mnc <outfile>.mnc
Mincreshapes main job is to chop a hyperslab out of a minc file and
put it into a new minc file. "What is a hyperslab?", you ask. It is
simply a multi-dimensional box specified with a starting index (a
vector giving a voxel coordinate) and a count vector (a number of
voxels along each axis). A single slice out of a volume is a hyperslab
(with a count of 1 in the slice direction), a small block pulled out of
a large volume is a hyperslab, a single echo volume out of a multi-echo
MRI dataset is a hyperslab, one time point out of a dynamic acquisition
is a hyperslab - you get the idea. Check out the -start, -count and
-dimrange options for more details on how to do this (and look at the
examples!). If you are pulling out only one point along a dimension,
you have the option of making the dimension disappear, so mincreshape
gives you the ability to reduce the dimensionality of a minc file. As
well, you aren’t constrained to specify a hyperslab that is only within
the input file, you can extend beyond the bounds of the dimensions in
the input file, and furthermore you can give a count that will flip the
data along a dimension.
As if all that is not enough, mincreshape has the ability to re-order
dimensions. The most obvious case is converting a transverse image into
a coronal image. But you can type a list of dimension names to get an
arbitrary order of dimensions.
You want more!?! Okay, okay. Mincreshape makes all of the minc library
ICV operations available on the command line. For those who like things
defined, an ICV is an image conversion variable (don’t ask me why I
called it that) which basically lets you tell the data what it’s going
to look like. In other words, it does a bunch of conversions for you.
These conversions include changing type, range and normalization of the
voxel values, expanding or contracting images (by voxel duplication or
averaging) to give a specified image size, and converting vector images
Just so you don’t get confused let me tell you clearly here:
mincreshape does all of the ICV conversions first and then the
hyperslab and dimension re-ordering stuff is applied to the result of
that. So if you want to mix them together (like -imgsize, -start,
-count), get it clear in your head first.
Okay, hold on to your seat: here’s a list of options.
Note that options can be specified in abbreviated form (as long as they
are unique) and can be given anywhere on the command line.
-2 Create MINC 2.0 format output files.
Overwrite an existing file.
Don’t overwrite an existing file (default).
Print out progress information for each chunk of data copied
(default). A chunk varies in size depending mostly on whether
you’re re-ordering dimensions or not and how big the internal
buffer is allowed to be.
-quiet Do not print out progress information.
Specify the maximum size of the copy buffer (in kbytes). Default
is 4096 kbytes (4meg).
Image conversion options (pixel type and range):
The default for type, sign and valid range is to use those of the input
file. If type is specified, then both sign and valid range are set to
the default for that type. If sign is specified, then valid range is
set to the default for the type and sign.
Don’t do any type conversion (default).
-byte Store output voxels in 8-bit integer format.
-short Store output voxels in 16-bit integer format.
-int Store output voxels in 32-bit integer format.
-long Superseded by -int.
-float Store output voxels in 32-bit floating point format.
Store output voxels in 64-bit floating point format.
Write out values as signed integers (default for short and
long). Ignored for floating point types.
Write out values as unsigned integers (default for byte).
Ignored for floating point types.
-valid_range min max
specifies the valid range of output voxel values in their
integer representation. Default is the full range for the type
and sign. This option is ignored for floating point values.
-image_range min max
Normalize images to a given minimum and maximum real value (not
Normalize images to real minimum and maximum for the entire
Do not normalize images (default).
Do not convert out-of-range values in input file, just copy them
Replace out-of-range values in input file by the smallest
possible value (default).
Specify a new pixel value to replace out-of-range values in the
Image conversion options (dimension direction and size):
Convert vector images to scalar images (a vector image is one
with vector_dimension as the fastest varying dimension). The
vector dimension is removed and values are averaged.
Do not convert vector images to scalar images (default).
Flip images to give positive step value for spatial axes. Note
that the flipping of spatial axes only applies to "image
dimensions". These are the two fastest varying (non-vector)
dimensions in the file. If you want to flip a non-image
dimension, you can convert it to an image dimension with
-dimsize dimname=-1 (the -1 means don’t really change the size).
Check out the examples.
Flip images to give negative step value for spatial axes.
Don’t flip images along spatial axes (default).
Flip images to give positive xspace:step value (left-to-right).
Flip images to give negative xspace:step value (right-to-left).
Don’t flip images along x-axis.
Flip images to give positive yspace:step value (posterior-to-
Flip images to give negative yspace:step value (anterior-to-
Don’t flip images along y-axis.
Flip images to give positive zspace:step value (inferior-to-
Flip images to give negative zspace:step value (superior-to-
Don’t flip images along z-axis.
Preserve aspect ratio when resizing images. This means that
voxels are replicated (or averaged) the same number of times
along each image dimension.
Do not force preservation of aspect ratio when resizing images
Specify the desired image size (used if -rowsize or -colsize not
Specify the desired number of rows in the image.
Specify the desired number of columns in the image.
Specify the size of a named dimension (dimension=size). Note
that the resizing only applies to "image dimensions" - usually
the two fastest-varying (non-vector) dimensions. To do dimension
resizing, all fastest-varying dimensions up to the named
dimension are turned into image dimensions, and these are then
affected by the direction options. The dimension name and size
must be in one command-line argument, so if you use spaces
(which is okay), remember to use quotes to hide them from the
Write out transverse slices.
Write out sagittal slices.
Write out coronal slices.
Specify dimension order, where dim? are the names of the
dimensions. You can give fewer dimensions than exist in the
file: they are assumed to be the fastest varying dimensions in
the output file (so -transverse is exactly equivalent to
-dimorder zspace,yspace,xspace). Again, spaces are allowed
between names, but remember to hide them from the shell with
Specify the range of dimension subscripts for dimension dim. If
count is missing or 0, then it is taken to mean 1, but remove
the dimension from the output file (a count of 1 will keep a
dimension of size 1). A negative count means flip the data along
that dimension - in this case start specifies the highest voxel
coordinate for the dimension (-dimrange xspace=3,-3 gives a
flipped version of -dimrange xspace=1,3). The options -start and
-count provide an alternative way to specify the same
Specifies the starting corner of the hyperslab (coordinates go
from slowest varying dimension to fastest). If fewer coordinates
are given than dimensions exist in the file, then they are
assumed to apply to the slowest varying dimensions and the
remaining coordinates are set to 0. See -dimrange for more
details. Both -start and -count give vectors that correspond to
input file dimensions after the image conversion (ICV) options
have been applied.
Specifies edge lengths of hyperslab to read (coordinates go from
slowest varying dimension to fastest). If fewer sizes are given
than dimensions exist in the file, then they are assumed to
apply to the slowest varying dimensions and the remaining sizes
are set to the full size of the dimension. See -dimrange for
more details. Both -start and -count give vectors that
correspond to input file dimensions after the image conversion
(ICV) options have been applied.
Missing data options:
Use value zero for points outside of the input volume (default).
-fill Use a fill value for points outside of input volume (minimum
Specify a fill value for points outside of the input volume
(this is a real value, not a pixel value).
Generic options for all commands:
-help Print summary of command-line options and exit.
Print the program’s version number and exit.
Assume that we have a volume with dimensions zspace, yspace, xspace
(that’s transverse) and sizes 128, 256, 256. If we want to get slice 40
out of it (keeping the coordinate information for the zspace
dimension), then we can use
mincreshape original.mnc new.mnc -dimrange zspace=40,1
Alternatively, we could use
mincreshape original.mnc new.mnc -start 40,0,0 -count 1,256,256
mincreshape original.mnc new.mnc -start 40 -count 1
If we wanted to get rid of the zspace dimension, we could use
mincreshape original.mnc new.mnc -dimrange zspace=40,0
Let’s get a block out of the middle and flip it along xspace:
mincreshape original.mnc new.mnc \
-start 40,10,240 -count 1,200,-200
But why restrain outselves? Let’s go out of bounds:
mincreshape original.mnc new.mnc \
-start 40,-100,340 -count 1,200,-200
If you want a sagittal volume, use this:
mincreshape original.mnc new.mnc -sagittal
How about some sideways heads - flip x and y. And convert to byte to
save space while we’re at it:
mincreshape original.mnc new.mnc -dimorder xspace,yspace -byte
You like to store volumes in x,y,z order (that’s z varying fastest! I
know some people who do it!)? Okay.
mincreshape original.mnc new.mnc -dimorder xspace,yspace,zspace
But you’re a minimalist (and don’t mind taking a chance). Here’s the
same thing (but it might break for another file):
mincreshape original.mnc new.mnc -dimorder zspace
Let’s make sure that all dimensions have a negative step attribute (see
option +direction for some details):
mincreshape original.mnc new.mnc -direction -dimsize zspace=-1
Copyright © 1994 by Peter Neelin
$Date: 2004-05-20 21:52:09 $