Hi all,
Thank you for the amaizing tool to use first of all.
I am trying to make 3d image from 2d image mouse brain slices, but somehow it keeps saying the same problem.
I followed the youtube tutorials from the beginning and I think I did everything correctly but it just shows this.
Could anyone please tell me what is wrong and what I can do to fix this?
Thank you in advance!
Running elastix with parameter file 1: "C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_BSpline_UL.txt".
Current time: Tue Oct 29 14:37:32 2024.
Reading the elastix parameters from file ...
ELASTIX version: 5.000
Command line options from ElastixBase:
-f C:/Users/A09behaviour/Desktop/Sample Images/3_Registered_Sections/DAPI_25.tif
-m C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017/Template.tif
-fMask unspecified, so no fixed mask used
-mMask unspecified, so no moving mask used
-out C:\Users\A09behaviour\Desktop\Sample Images\5_Analysis_Output\Temp\Template_aligned
-p C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_Affine.txt
-p C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_BSpline_UL.txt
-priority unspecified, so NORMAL process priority
-threads unspecified, so all available threads are used
Command line options from TransformBase:
-t0 unspecified, so no initial transform used
WARNING: The parameter "BSplineTransformSplineOrder", requested at entry number 0, does not exist at all.
The default value "3" is used instead.
WARNING: The parameter "UseCyclicTransform", requested at entry number 0, does not exist at all.
The default value "false" is used instead.
Reading images...
Reading images took 0 ms.
WARNING: the fixed pyramid schedule is not fully specified!
A default pyramid schedule is used.
WARNING: the moving pyramid schedule is not fully specified!
A default pyramid schedule is used.
Initialization of all components (before registration) took: 9 ms.
Preparation of the image pyramids took: 2673 ms.
Resolution: 0
WARNING: The parameter "UseMultiThreadingForMetrics", requested at entry number 0, does not exist at all.
The default value "true" is used instead.
Setting the fixed masks took: 0 ms.
Setting the moving masks took: 0 ms.
itk::ExceptionObject (00000012B82FF340)
Location: "ElastixTemplate - Run()"
File: f:\x\src\elx\elastix\components\imagesamplers\randomcoordinate\elxRandomCoordinateSampler.hxx
Line: 113
Description: itk::ERROR: RandomCoordinateSampler(0000015A0630D8B0): ERROR: in your parameter file you selected
SampleRegionSize[ 2 ] = 100 mm,
while the fixed image size at dim = 2 is 34 voxels or 34 mm.
Please select a smaller SampleRegionSize!
It is recommended to be not larger than 1/3 of the image size in mm.
Error occurred during actual registration.
Errors occurred!
Hi all,
Thank you for the amaizing tool to use first of all.
I am trying to make 3d image from 2d image mouse brain slices, but somehow it keeps saying the same problem.
I followed the youtube tutorials from the beginning and I think I did everything correctly but it just shows this.
Could anyone please tell me what is wrong and what I can do to fix this?
Thank you in advance!
Running elastix with parameter file 1: "C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_BSpline_UL.txt".
Current time: Tue Oct 29 14:37:32 2024.
Reading the elastix parameters from file ...
ELASTIX version: 5.000
Command line options from ElastixBase:
-f C:/Users/A09behaviour/Desktop/Sample Images/3_Registered_Sections/DAPI_25.tif
-m C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017/Template.tif
-fMask unspecified, so no fixed mask used
-mMask unspecified, so no moving mask used
-out C:\Users\A09behaviour\Desktop\Sample Images\5_Analysis_Output\Temp\Template_aligned
-p C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_Affine.txt
-p C:/Users/A09behaviour/Desktop/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_BSpline_UL.txt
-priority unspecified, so NORMAL process priority
-threads unspecified, so all available threads are used
Command line options from TransformBase:
-t0 unspecified, so no initial transform used
WARNING: The parameter "BSplineTransformSplineOrder", requested at entry number 0, does not exist at all.
The default value "3" is used instead.
WARNING: The parameter "UseCyclicTransform", requested at entry number 0, does not exist at all.
The default value "false" is used instead.
Reading images...
Reading images took 0 ms.
WARNING: the fixed pyramid schedule is not fully specified!
A default pyramid schedule is used.
WARNING: the moving pyramid schedule is not fully specified!
A default pyramid schedule is used.
Initialization of all components (before registration) took: 9 ms.
Preparation of the image pyramids took: 2673 ms.
Resolution: 0
WARNING: The parameter "UseMultiThreadingForMetrics", requested at entry number 0, does not exist at all.
The default value "true" is used instead.
Setting the fixed masks took: 0 ms.
Setting the moving masks took: 0 ms.
itk::ExceptionObject (00000012B82FF340)
Location: "ElastixTemplate - Run()"
File: f:\x\src\elx\elastix\components\imagesamplers\randomcoordinate\elxRandomCoordinateSampler.hxx
Line: 113
Description: itk::ERROR: RandomCoordinateSampler(0000015A0630D8B0): ERROR: in your parameter file you selected
SampleRegionSize[ 2 ] = 100 mm,
while the fixed image size at dim = 2 is 34 voxels or 34 mm.
Please select a smaller SampleRegionSize!
It is recommended to be not larger than 1/3 of the image size in mm.
Error occurred during actual registration.
Errors occurred!