EM Segmenter with Atlas

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EM Segmenter with Atlas

David Radoff

Hello,

 

I am trying to use the EMSegmenter with Atlas module to segment the hippocampus. No matter what I try, I always get the same error.   I’ve tried non-skull stripped SPGRs in both axial and sagittal views.  I’m using Slicer 4.3.1 on a 64-bit Windows 7 machine (16GB RAM).  Here are the options I’m using for the segmenter:

 

Part 1

Task: MRI Human Brain Full Parcellation, Advanced Mode

 

Part 2

Input Datasets: T1: <my SPGR>

Align input datasets: I’ve tried both checked and unchecked

 

Part 3

Using default tree, but I also tried adding nodes for the Left and Right hippocampi with no success

 

Part 4

Using default probability and parcellation maps

 

Part 5

T1: atlas_T1

Affine Registration: Accurate

Deformable Registration: Accurate

Interpolation: Linear

Registration Package: BRAINS

 

Part 6

Register atlas to input scan: I’ve tried checked and unchecked

Perform image inhomogeneity correction on input scan: I’ve tried checked and unchecked, but ideally this should be checked I think

 

Preprocessing runs for about 4-5 minutes, and then I get an error message that says “Pre-processing did not execute correctly!”.  This occurs no matter which options I try.  Do you have any suggestions about what’s causing the problem and how to fix it?  Also, is this the best method to segment the hippocampus in Slicer, or is there a better way?  I would appreciate any help.

 

Thank you,

 

David

 


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Re: EM Segmenter with Atlas

Kilian Pohl
This is a windows specific issue - Please review

http://na-mic.org/Mantis/view.php?id=3561

We are investigating

Kilian

On 3/12/2014 1:07 PM, David Radoff wrote:

Hello,

 

I am trying to use the EMSegmenter with Atlas module to segment the hippocampus. No matter what I try, I always get the same error.   I’ve tried non-skull stripped SPGRs in both axial and sagittal views.  I’m using Slicer 4.3.1 on a 64-bit Windows 7 machine (16GB RAM).  Here are the options I’m using for the segmenter:

 

Part 1

Task: MRI Human Brain Full Parcellation, Advanced Mode

 

Part 2

Input Datasets: T1: <my SPGR>

Align input datasets: I’ve tried both checked and unchecked

 

Part 3

Using default tree, but I also tried adding nodes for the Left and Right hippocampi with no success

 

Part 4

Using default probability and parcellation maps

 

Part 5

T1: atlas_T1

Affine Registration: Accurate

Deformable Registration: Accurate

Interpolation: Linear

Registration Package: BRAINS

 

Part 6

Register atlas to input scan: I’ve tried checked and unchecked

Perform image inhomogeneity correction on input scan: I’ve tried checked and unchecked, but ideally this should be checked I think

 

Preprocessing runs for about 4-5 minutes, and then I get an error message that says “Pre-processing did not execute correctly!”.  This occurs no matter which options I try.  Do you have any suggestions about what’s causing the problem and how to fix it?  Also, is this the best method to segment the hippocampus in Slicer, or is there a better way?  I would appreciate any help.

 

Thank you,

 

David

 



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-- 
Kilian M. Pohl

Senior Research Scientist
SRI International 

Consulting Assistant Professor
Department of Psychiatry and Behavioral Sciences
Stanford

333 Ravenswood Ave
Menlo Park, CA 94025 

Cell: (831) 247 2275
Fax:  (650) 859-2743 

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contains patient information, please contact the Partners Compliance HelpLine at
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