abpBrainExtraction creating non-head voxel mask about antsr HOT 5 CLOSED

looks like your brain mask has max values near 0.5

you should use a binary mask

also - see the ants cortical thickness paper for our philosophy on this (
custom templates )

brian

On Fri, Jun 12, 2015 at 11:40 AM, BrysonBR [email protected] wrote:

First, I want to say thanks for so quickly resolving my last
abpBrainExtraction issue, it worked. But, I used a crappy "tem" and
"temmask" so I got a crappy brain mask. In an effort to fix this I am
trying to use the MNI standard brain as the template and it's very good
brain mask as the template mask. I used the code below:

ImageMath 3 close_MP1.nii.gz ClosestSimplifiedHeaderMatrix MP1.nii.gz
ImageMath 3 close_MNI.nii.gz ClosestSimplifiedHeaderMatrix MNInew.nii.gz
ImageMath 3 close_MNImask.nii.gz ClosestSimplifiedHeaderMatrix
brainMask.nii

struct<-antsImageRead("/Users/Bryson/Data/ANTsR_test/close_MP1.nii.gz")
struct<-abpN4(struct)
tem<-antsImageRead("/Users/Bryson/Data/ANTsR_test/close_MNI.nii.gz")
tem<-abpN4(tem)

temmask<-antsImageRead("/Users/Bryson/Data/ANTsR_test/close_MNImask.nii.gz")

bm<-abpBrainExtraction(img=struct,tem=tem,temmask=temmask)

antsImageWrite(bm$bmask, "MP1bmask.nii.gz")
antsImageWrite(bm$brain, "MP1masked.nii.gz")

But the output I got looked more like a head-excluding mask than a
brain-including mask.

I've attached the input and output files here:

https://drive.google.com/open?id=0B9oWACI5TJOEfm1KdzAxSG5IdlNZR3QyOEtGa3l2ZEVETHBUQXZyNDJGUGk5YXRNT2N4blk&authuser=0

Thanks again for your help!

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#55.

from antsr.

You are correct, once I binarized the mask it ran well. I am getting an error, but it is not crashing and the output looks good. The error is:

bad det -1 v 1 u -1
bad det -1 v 1 u -1 new 1

I'm not sure if I should be worried about it or not.
I'll read that paper you suggested to get a better understanding of the templates, thanks again.

from antsr.

thats nothing to worry about.

brian

On Fri, Jun 12, 2015 at 2:46 PM, BrysonBR [email protected] wrote:

You are correct, once I binarized the mask it ran well. I am getting an
error, but it is not crashing and the output looks good. The error is:

bad det -1 v 1 u -1
bad det -1 v 1 u -1 new 1

I'm not sure if I should be worried about it or not.
I'll read that paper you suggested to get a better understanding of the
templates, thanks again.

—
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#55 (comment).

from antsr.

also, you may not have to use the "closest" trick with this setup i.e. when
mapping to MNI

brian

On Fri, Jun 12, 2015 at 2:47 PM, brian avants [email protected] wrote:

thats nothing to worry about.

brian

On Fri, Jun 12, 2015 at 2:46 PM, BrysonBR [email protected]
wrote:

You are correct, once I binarized the mask it ran well. I am getting an
error, but it is not crashing and the output looks good. The error is:

bad det -1 v 1 u -1
bad det -1 v 1 u -1 new 1

I'm not sure if I should be worried about it or not.
I'll read that paper you suggested to get a better understanding of the
templates, thanks again.

—
Reply to this email directly or view it on GitHub
#55 (comment).

from antsr.

Thanks, I appreciate all of your help and guidance.

from antsr.