users > RE: Registration of 32-bit stacks
Jul 31, 2020  06:07 AM | Francesco Vanzi
RE: Registration of 32-bit stacks
The reason I am trying this might be due to a very naive approach to the following problem:

I have a stack resulting from segmentation of my imaging original stack. The segmented data give me the neuron id number in each pixel occupied by that neuron. I want to register this segmented data to a reference brain. So, what I do is this:
1) I register the original greyscale stack to the reference brain
2) I use the xform file obtained in step 1 to register the segmented stack with neuron label numbers to the reference brain so I can read each neuron number directly in a referenced anatomical area. (In a previous post you helped me to solve the problem of registering labels rather than greyscale values by using the -pv option in reformatx)

Since neurons numbers exceed 65536 I need to go higher than 16 bit in the segmented stack.

Thanks for your help!

Francesco


Originally posted by Greg Jefferis:
Strange. Maybe try changing one or both images back to 16 or 8 bit and see if you are able to start things? In general I can't see a strong reason for using anything above 16 bit. Best, Greg,
Originally posted by Francesco Vanzi:
Originally posted by Greg Jefferis:
Can you run one of the individual registrations to get more info about the error. e.g.

cd C:\CMTK_Registration\CMTKreg

C:\CMTK_Registration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images/MIP318zf01.nrrd


I ran the command but there was no visible outcome

C:\CMTK_Registration\CMTKreg>C:\CMTK_Registration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images/MIP318zf01.nrrd
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.

Threaded View

TitleAuthorDate
Francesco Vanzi Jul 31, 2020
Francesco Vanzi Aug 1, 2020
Greg Jefferis Jul 31, 2020
Francesco Vanzi Jul 31, 2020
Greg Jefferis Jul 31, 2020
Francesco Vanzi Jul 31, 2020
Greg Jefferis Jul 31, 2020
RE: Registration of 32-bit stacks
Francesco Vanzi Jul 31, 2020
Greg Jefferis Aug 1, 2020
Francesco Vanzi Aug 1, 2020
Greg Jefferis Aug 1, 2020
Greg Jefferis Aug 1, 2020
Francesco Vanzi Aug 1, 2020
Greg Jefferis Aug 1, 2020
Francesco Vanzi Aug 1, 2020
Greg Jefferis Aug 1, 2020
Francesco Vanzi Aug 7, 2020