Register in space (and other t4 oriented programs)
imgreg_4dfp
compute transform (various modes)
Usage:
imgreg_4dfp target_imag target_mask source_imag source_mask t4file mode
imgreg_4dfp target_imag none source_imag source_mask t4file mode
imgreg_4dfp target_imag none source_imag none t4file mode
Mode options
1 |
enable coordinate transform |
2 |
enable 3D alignment |
4 |
enable affine warp (12 parameters in 3D 6 parameters in 2D) |
8 |
enable voxel size adjust |
16 |
disable x voxel size adjust |
32 |
disable y voxel size adjust |
64 |
disable z voxel size adjust |
128 |
unassigned |
256 |
when set use difference image minimization (for similar contrast mechanisms) |
512 |
superfine mode (2 mm cubic grid metric sampling) |
1024 |
fast mode (12 mm cubic grid metric sampling) |
2048 |
fine mode (5 mm cubic grid metric sampling) |
4096 |
[T] restricted to translation explored at 7.5 mm intervals |
8192 |
enable parameter optimization by computation of the metric gradient in parameter space and inversion of the Hessian |
t4imgs_4dfp
apply transforms, resample and average (list directed)
Usage: t4imgs_4dfp [options] <inlist> <outfile>
Example inlist:
<imgfile1> t4=<t4_file1>
<imgfile2> t4=<t4_file2>
<imgfile3> t4=<t4_file3>
Options
-z |
normalize by sqrt(n) rather than n (for z images) |
-s |
interpolate by 3D cubic spline (default is 3D linear) |
-N |
output NaN (default 0.0) for undefined values |
-B |
internally convert to_711-2A_t4->to_711-2B_t4 |
-n |
use nearest neighbor interpolation |
-R |
suppress creation of rec file |
-O111 |
output in 111 space instead of default 333.0 space |
-O222 |
output in 222 space instead of default 333.0 space |
-O333.n |
output in 333.n space (y shifted up by n pixels) |
-Omy_image |
duplicate dimensions of my_image.4dfp.ifh |
-@<b|l> |
output big or little endian (default CPU endian) |
t4img_4dfp
single image wrapper for t4imgs_4dfp
Usage: t4img_4dfp <t4file> <imgfile> [outfile]
Examples:
t4img_4dfp vce1_mprS_to_711-2B_t4 vce1_mprS.4dfp.img -O222
t4img_4dfp vce1_mprS_to_711-2B_t4 vce1_mprS vce_mprS_711-2B -O222
t4img_4dfp none vce1_mprS vce1_mprS_222 -O222
Options
-z |
normalize by sqrt(n) rather than n (for z images) |
-s |
interpolate by 3D cubic spline (default is 3D linear) |
-N |
output NaN (default 0.0) for undefined values |
-B |
internally convert to_711-2A_t4->to_711-2B_t4 |
-n |
use nearest neighbor interpolation |
-R |
suppress creation of rec file |
-O111 |
output in 111 space instead of default 333.0 space |
-O222 |
output in 222 space instead of default 333.0 space |
-O333.n |
output in 333.n space (y shifted up by n pixels) |
-Omy_image |
duplicate dimensions of my_image.4dfp.ifh |
-@<b|l> |
output big or little endian (default CPU endian) |
outfile |
specify name for output file (default is <imgfile>t) |
N.B.: 4dfp filename extensions are optional N.B.: option -n causes fidl ROI names to be copied to the output ifh
wrpsmg_4dfp
apply transforms, resample and average difference images (list directed)
Usage: wrpsmg_4dfp [options] <inlist> <outfile>
Options
-N |
output NaN (default 0.0) for undefined values |
-w |
create sum of weights image |
-s |
create square root variance (sd) image |
-O111 |
output in 111 space |
-O222 |
output in 222 space (default) |
-O333.n |
output in 333.n space (y shifted up by n pixels) |
-Omy_image |
duplicate dimensions of my_image.4dfp.ifh |
-@<b|l> |
output big or little endian (default CPU endian) |
stretch_out
remove transform stretch
Usage: stretch_out <t4file> [t4file_new]
N.B.: default output filename is <t4file>”r”
t4_mul
compose transforms
Usage: t4_mul <left_t4file> <right_t4file> [product_t4file]
Examples:
t4_mul vm11b_anat_ave_to_vm11b_234-3_t4 vm11b_234-3_to_711-2B_t4 [vm11b_anat_ave_to_711-2B_t4]
t4_inv
invert transform
Usage: t4_inv <t4file> [inv_t4file]
Examples:
t4_inv vm11b_anat_ave_to_vm11b_234-3_t4 [vm11b_234-3_to_vm11b_anat_ave_t4]
Options
-u |
suppress (intensity) scale field in output |
t4_factor
decompose affine transform into components (translation, rotation, stretch)
Usage: t4_factor <t4file>
Examples:
t4_factor vm11b_anat_ave_to_vm11b_234-3_t4
t4_null
create an identity transform t4 file
Usage: t4_null <t4file>
Examples:
t4_null vm11b_mpr1_to_711-2B_t4
t4_resolve
compute optimal rigid body transforms connecting a set of images
Usage: t4_resolve <image1> <image2> …
Options
-v |
verbose mode |
-m |
generate mat file output |
-s |
include intensity scale factor in t4 file output |
-w |
weight inversely in proportion to scale in sub file output (sum counts mode) |
-o<str> |
write resolved output with specified fileroot |
-r<flt> |
set VOI rms radius in mm (default=50) |
N.B.: t4_resolve looks for t4 files <image1>_to_<image2>_t4, <image1>_to_<image3>_t4, … N.B.: t4_resolve automatically strips filename extensions when constructing t4 filenames
t4_pts
inter-convert coordinates, e.g., 711-2B \(\leftrightarrow\) MNI152
Usage: t4_pts <t4file> <pts.lst> [new pts.lst]
Examples:
t4_pts 711-2B_to_MNI152lin_T1_t4 711-2B_coords MNI152_coords