JRC2018_Unisex_20x_HR template

[ibrahimtastekin]

Hi,

I have been trying to use the neuronbridge using colordepth MIP masks. When I used JRC2018_UNISEX_38um_iso_16bit the search does not give any hits.

On the neuronbridge website it is stated that JRC2018_Unisex_20x_HR template should be used. I was wondering whether the resolution difference between these templates would lead to the failure to get any hits.

I cannot find the JRC2018_Unisex_20x_HR template on https://www.janelia.org/open-science/jrc-2018-brain-templates to register my LM stacks. I wonder if you could help me download it.

Thanks
Ibo

[bogovicj]

I was wondering whether the resolution difference between these templates would lead to the failure to get any hits.

It will not, as long as the transformations are done correctly.

However, for convenience's sake, I will publish the JRC2018_Unisex_20x_HR template on figshare and will post back here once it's up.

Thanks for reporting this, and your interest.

[ibrahimtastekin]

Thanks John!

Initially I tried to use JRC 2018 Unisex - JFRC 2010 transform on https://www.janelia.org/open-science/jrc-2018-brain-templates to register JFRC2 to JRC2018_UNISEX_38um_iso_16bit but it resulted in a shift in z. I think the voxel size on the z-dimension in JFRC2010 you used is not the same as JFRC2 I used (downloaded from VFB).

Therefore I decided to create my own transform using Ants to register JFRC2 to JRC2018_UNISEX_38um_iso_16bit.

Here is the script I used:

`fixed=$1
moving=$2
output=$3

antsRegistration
-d 3
-v 1
-o [${output}, ${output}.nii]
--initial-moving-transform [${fixed},${moving},1]
--interpolation linear
--use-histogram-matching 1
-t rigid[0.5]
-m MI[${fixed},${moving},1,32,Regular,0.25]
-c [200x200x200x0,1e-7,10]
-f 8x4x2x1
-s 3x2x1x0vox
--transform Affine[0.1]
--metric MI[${fixed},${moving},1,32,Regular,0.25]
--convergence [1000x1000x250x100,1e-6,10]
--shrink-factors 8x4x2x1
--smoothing-sigmas 3x2x1x0vox
--transform SyN[0.1,3,0]
--metric CC[${fixed},${moving},1,4]
--convergence [200x70x50x20,1e-7,10]
--shrink-factors 8x4x2x2
--smoothing-sigmas 3x2x1x0vox `

I wonder if you could kindly have a look at my transform if I send it to you. Let me know!

Thanks
Ibo