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help > BrainAligner : displacement field
Jul 10, 2011 11:07 AM | Thomas Templier
BrainAligner : displacement field
Hello,
I would like to compute a transformation from one brain to another, and save this transformation. I would like to apply this transformation later to other channels. (there is already a tool to apply the transformation to attached channels, but I'm dealing with images with channels already splitted).
To use a displacement field, it should be like this I suppose :
But I can't find how to create this displacement field. Anybody knows ?
Thank you
Best Regards
Thomas Templier
The help of BrainAligner :
I would like to compute a transformation from one brain to another, and save this transformation. I would like to apply this transformation later to other channels. (there is already a tool to apply the transformation to attached channels, but I'm dealing with images with channels already splitted).
To use a displacement field, it should be like this I suppose :
jba_redhat -s subject.tif -F
displacement_field.raw -o output.tif
But I can't find how to create this displacement field. Anybody knows ?
Thank you
Best Regards
Thomas Templier
The help of BrainAligner :
Usage: jba -t -s -o -c -w
-n
-t .raw/.tif file
containing 3D template/target stack to which a subject image will
be warped/mapped.
-s .raw/.tif file
containing 3D subject which will deform/warp to best appriximate
the geometry of the template/target.
-o .raw/.tif file
containing warped result stack.
-F .raw file (4-byte
float) containing the displacement field (DF), chanel 0, 1, 2 for
sx, sy, ans sz in terms of pixels.
Note: specify -t will
prohibit -F.
-L a plain text csv file
containing landmarks of only the target_pos (if -w 9).
-l a plain text csv file
containing landmarks of only the subject_pos (if -w 9). If
un-specified, then assume -w 6
[-C] the ID of the
reference channel of the target image (default 0) which is used in
computing warping.
[-c] the ID of the
reference channel of the subject image (default 0) which is used in
computing warping. All other channels will use the same
warp.
[-w] the type of warp, 0
-- global, 10 -- for landmark-based local matching (assumed
globally aligned).
[-n] number of loops of
global/local estimation.
[-m] number of loops of
local smoothing.
[-z] minimal xy size in
the pyrimid (e.g. 64 or 32).
[-r] the half window size
in defining the local block (e.g. 5 means a 11x11 block, and 3
means a 7x7 block).
[-X] target image: X/Y
direction pixel size (resolution) in microns. Also assume the X and
Y pixel size are always the same.
[-Z] target image: Z
direction resolution in microns.
[-U] subject image: X/Y
direction pixel size (resolution) in microns. Also assume the X and
Y pixel size are always the same.
[-V] subject image: Z
direction resolution in microns.
[-B] XY plane size of
image mapping (default is 512, can be 1024, 2048, or 256, - note:
if use 1024 and above, should use the cluster node with big
memory).
[-e] multiplication factor
for control points in an existing landmark file (e.g. if image size
is 1024, and existing landmarks are defined using 512 image, then
use -e 2. Default is 1.).
[-j] set landmark matching
method (0: MI; 1: RLM (MI+Intensity+CORR); 2: Intensity; 3:
CORR).
[-i] set displacement
generation method (0: TPS; 1: TPS-linear; 2: TPS-B_spline; 3:
B_spline. Default is 1).
[-H] hierarchical matching
level. Default is 1, i.e. no matching at downsampled domain. If set
to >=2, then finding the matching points on downsampled images
first and then refine the search at the original
resolution.
[-T] only convert the file
format of the -s file to the -o file (if they have the same
suffixes, then just a save as).
[-A] attaching a channel
of the target image to a channel of the warped subject. This option
specifies the channel of the Target image to transfer. Default not
attach, unless both -A and -a are set.
[-a] attaching a channel
of the target image to a channel of the warped subject. This option
specifies the channel of the subject image to copy to. Default do
not attach, unless both -A and -a are set
[-R] do resampling to
default 0.58/0.8.
[-v] verbose printing
enabled.
[-h] print this
message.
JBA version: 0.82 (as of
Nov 9, 2010).
Threaded View
| Title | Author | Date |
|---|---|---|
| Thomas Templier | Jul 10, 2011 | |
| Hanchuan Peng | Jul 11, 2011 | |
| Thomas Templier | Jul 12, 2011 | |
| Hanchuan Peng | Jul 13, 2011 | |
| Thomas Templier | Aug 5, 2011 | |
| Hanchuan Peng | Aug 6, 2011 | |
| Thomas Templier | Aug 8, 2011 | |
| Hanchuan Peng | Aug 8, 2011 | |
| Thomas Templier | Aug 8, 2011 | |
| Hanchuan Peng | Aug 9, 2011 | |
| Thomas Templier | Aug 9, 2011 | |