Gabriel A. Devenyi
Gabriel A. Devenyi
> I also noticed that contrast range of the anatomical image is pretty heavily truncated. Metadata says the file is post-Freesurfer, so its had lots of manipulation done to it
This is going to be a tough problem. My suggestion is to 1. Ensure you have good brain masks and skullstrip 2. Try my registration scripts: https://github.com/CoBrALab/minc-toolkit-extras/blob/master/antsRegistration_affine_SyN.sh (dependecy) https://github.com/CoBrALab/minc-toolkit-extras/blob/master/ants_generate_iterations.py Which...
You need to have a copy of the script, it needs to be `chmod +x` and it needs to be on the PATH. I suggest you git clone the repo...
> This is my command： You are overrriding all the automatic features. Just use: `antsRegistration_affine_SyN.sh --syn-control 0.25,3,0 dogbrain46_brain.nii.gz begle_Deformable_template0_rigid.nii.gzWarped.nii.gz testCC3_0.25_`
Hi, First, I think you may be running into violating the fundamental assumptions of image registration, that the anatomy present in each image has a 1:1 correspondence, allowing for in-theory...
What I'm proposing is the -x option generalize to floating point numbers to weight the registration rather than an include/exclude
Got it @stnava I missed your earlier comment. I'll move this up to ITK
Upstreamed, https://github.com/InsightSoftwareConsortium/ITK/issues/3704
Ref: #1299 https://github.com/freesurfer/freesurfer/pull/1386
> adding a dependency on using the h5repack command. This only needs to happen once to re-pack the weights in the repo. There is no added dependency. > filter plugins...