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License: Other
Extra miscellaneous scripts for minc-toolkit
License: Other
Print a warning if both images are not masked, but there's no reason we can't extract only the moving or only the fixed if provided.
This comes up for things like CBF->T1 and similar, where one of the images has no skull signal intrinsicly
Hi @gdevenyi
Running antsRegistration_affine_SyN.sh
in a Singularity image. Installed from current Github as of last week. I get the following after stage 3 (AffineTransformation):
antsRegistration_affine_SyN.sh $TPL ${initmask}/mean_bzero.nii.gz ${initmask}/tpl2dwi_ --fast --moving ${initmask}/tpl_lap_norm.nii.gz --fixed ${initmask}/mean_bzero_lap_norm.nii.gz
...
/opt/minc-toolkit-extras/antsRegistration_affine_SyN.sh: line 860: _arg_weights[$((i+1))]: unbound variable
All files exist. I can run registration between the TPL and mean_bzero as well as *lap_norm files independently, just not as multispectral.
Any thoughts? Is it because weights isn't specified (I just thought of that as I wrote it...)
Hi,
I'm sorry for asking , in the command instruction :
antsRegistration_affine_SyN.sh [...]\
--fixed multi_f1 --moving multi_m1\
--fixed multi_f2 --moving multi_m2 \
--weights 0.1,0.2, 0.7 [....]\
<movingfile_m0> <fixedfile_f0> <outputbasename>
A single value, which disables weighting, or a comma separated list of weights, ordered primary pair, followed by multispectral pairs
so if I define --weights 0.1,0.2,0.7
movingfile_m0 fixedfile_f0
are the primary pair, weight will be 0.1
and [--fixed <multi_f1] [--moving multi_m1]
are the first multispectral pairs, weight will be 0.2
and [--fixed <multi_f2] [--moving multi_m2]
are the first multispectral pairs, weight will be 0.7
Is it true or the opposite ?
Thanks in advance,
Valéry
Or at least throw an error.
Command run :
./create_morpho_image.sh new_lefthc.obj ../lm/tvalue_CA_left_icv.csv 2.17406767435032,2.83736873702781 new_righthc.obj ../lm/tvalue_CA_right_icv.csv 2.28660590804178,2.96056946858748 tvalue-groupcatCTRL ../morpho_images/lm_CA_icv.png &> create_morpho_image.log
I'm getting the thresholds automatically, that's why the long format. Using "normal" format does not change the issue.
The two csv files have the tvalue-groupcatCTRL
column.
Content of create_morpho_image.log :
Value range: -10.3427 9.13157
Value range: -10.3427 9.13157
Value range: -8.1667 6.80638
Value range: -8.1667 6.80638
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
Ray Tracing: ..................................................................
/tmp/tmp.HtXGFYoNLc
Content of TMPDIR :
1.png
2.png
3.png
4.png
back.png
back.rgb
bottom.png
bottom.rgb
coldmetalinv.png
front.png
front.rgb
left_comb.obj
left_lateral.png
left_lateral.rgb
left_medial.png
left_medial.rgb
left_pos.obj
redmetalinv.png
right_comb.obj
right_lateral.png
right_lateral.rgb
right_medial.png
right_medial.rgb
right_pos.obj
rmincblue.map
rmincred.map
top.png
top.rgb
tvalue_CA_left_icv.csv
tvalue_CA_right_icv.csv
unlabelled.png
lm_CA_icv.png
unlabelled.png
First, thanks for all of the exceptionally cool improvements you make to existing programs. ants_generate_iterations.sh
and antsRegistration_affine_SyN.sh
are fantastic and have dramatically improved not only my mouse templates but also the registration of those templates to standard spaces.
Two things:
antsRegistration_affine_SyN.sh
. Is it as simple as antsRegistration_affine_SyN.sh $moving $fixed dwi2struct_ --skip-nonlinear --linear-type rigid
?bc might not be available
Need to fix paths for supporting datafiles.
Could you please share the python environment required to run the t2star_fit.py and t2star_fit_simpleitk.py functions?
I'm running into several issues when trying to install the imported packages one by one.
Thanks.
Multispectral registration fails because the weight array isn't properly specified
Hello! I am hoping to use ants_generate_iterations.py
to construct a more robust group template, but I am unsure what the --min
and --max
arguments are referring to. Are they referring to dimensions of the input images, or the dimensions of the voxels in the input images? Or something else?
antsRegistration_affine_SyN
ants_generate_iterations
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