cat skull stripe

AFNI Message Board
1

Hello,
I am trying to do skull stripe on cat’s brain. But there is no cats’ template, do you have some suggestions on by doing it on afni. I tried to modify the parameters on monkey’s template, but it didn’t work well.
Thanks.
Meizhen

2

I’ve never seen this in MRI images, but I was able to download a high-resolution cat MRI from the link below and script this to work with that dataset.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060963/

There is also this recent paper that produced a group template, but I don’t see where that is publicly available.
https://www.frontiersin.org/articles/10.3389/fvets.2018.00172/full

#!/bin/tcsh

3dCatSkin

skullstripping for cat MRI

example with MPRage dataset downloaded from here:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060963/

Heather L. Gray-Edwards, et al, High resolution MRI anatomy of the cat brain at 3 Tesla,

J. Neuroscience Methods. 2014 Apr 30; 227: 10–17.

mv 3D\ MPRage.nii.gz 3DMPrage.nii.gz
3dcopy 3DMPrage.nii.gz cat_MP

fix the orientation of this data (it’s wrong in the distributed header)

edited here to add missing orientation code

3drefit -orient RPI cat_MP+orig

also make this cardinal

3drefit -deoblique cat_MP+orig

make temporary copy

3dcopy cat_MP+orig. cat_MP_temp_resize

change dimensions to scale this to more human size

3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 -keepcen cat_MP_temp_resize+orig.

strip skull as if it were human

3dSkullStrip -prefix cat_ns -input cat_MP_temp_resize+orig. -shrink_fac_bot_lim 2.0

restore original dimensions

3drefit -xdel 0.417 -ydel 0.417 -zdel 0.4 -keepcen cat_ns+orig

3

Hi Daniel,

Thanks for your information. That’s very nice of you.
Actually I tried doing skull stripe on monkey template, with fc from 0.1-0.2, it could run with single 3dSkullStripe, but it failed in align_epi_anat.py -anat2epi, for it could not do skullstripe in align’s default option. My purpose is to do resting connectivity analysis, now got stuck in this step.

Thanks.
Meizhen

4

Did you try the steps I suggested for the cat? 3dSkullStrip has defaults for humans. The other animal options there do a similar resizing trick inside the program.

5

You forgot to include the orientation in your 3drefit command. :slight_smile: I believe it should either be RPI or LPI.

6

Hi Daniel,

Thanks very much for your information. It’s helpful. I tried and it turned out to be much better!

Thanks,
Meizhen

7

Hi Phil,

Thanks very much, yes, I set it RPI and it worked!

Meizhen

8

Hi Daniel,

I used the resize tricky to do the skull-stripe, it looks nice, but when I check the alignment, I found that the brain size in epi and structure images were not the same. I resized the 0.5mm isotropic structure images to 1mm isotropic and 1mm isotropic original epi images to 2mm isotropic. What went wrong?
Thanks for your patience and kind help.

Meizhen

9

I’m not clear what is wrong here. Can you post the exact commands you used and what you think is wrong?