I am trying to use the BrainAligner function but cannot seem to get it to work.

C:\Program Files\Vaa3D-3.20\bin>vaa3d /x brainaligner /f brainaligner /p "#t  #s  #w <10>"
Qt: Untested Windows version 6.2 detected!
[vaa3d]
[/x]
[brainaligner]
[/f]
[brainaligner]
[/p]
[#t #s #w <10>]
>>key ... /x
call plugin ... brainaligner
>>key ... /f
call plugin function ... brainaligner
>>key ... /p
Searching in ./plugins ......
Searching ./plugins done.
Current canonical path = [brainaligner]
Searching in ./plugins ......
Searching ./plugins done.
plugins
callPluginFunc fullpath: "C:/Program Files/Vaa3D-3.20/bin/plugins/image_registration/brainaligner/brainaligner.dll"
You have not specified the subject image or the output image. Do nothing.
Fail to call plugin function.
**** the plugin preprocessing takes [ 172 milliseconds]

C:\Program Files\Vaa3D-3.20\bin>



I have tried calling the plugin using other syntax, though this is the only code that will give me the error 'you have not specified the subject image..". Otherwise I will receive an error "your input is illegal" when I use 'vaa3d /x brainaligner /f brainaligner /p /t test1.tif /s test2.tif /w 10', where /t is the illegal input.


C:\Program Files\Vaa3D-3.20\bin>vaa3d /x brainaligner /f brainaligner /p /t test1.tif /s test2.tif /w 10
Qt: Untested Windows version 6.2 detected!
[vaa3d]
[/x]
[brainaligner]
[/f]
[brainaligner]
[/p]
[/t]
[test1.tif]
[/s]
[test2.tif]
[/w]
[10]
>>key ... /x
call plugin ... brainaligner
>>key ... /f
call plugin function ... brainaligner
>>key ... /p
>>key ... /t
parsing ... t 6 Unknown command. Type 'vaa3d -h' for usage
Your input is illegal. Please follow the instruction of the help page below.



Is the program simply unable to find my images (they are on my desktop), am I calling the function incorrectly? I know there are syntax differences between Mac and Windows (I am using Windows). 

Any help would be appreciated, thank you!

Thanks for trying brainagliner.

The command line is 

/vaa3d -x brainaligner -f brainaligner -p "#t #s #o #w ... "

So you have to using "#" to label the flag and put all parameters in "" as a string for parsing. Hope this helps. Please let us know if you still have problems.

thanks,
Yang

It seems my input didnt fully copy over. Below is the command I am entering into the program (with the result that the subject image and output image was not specified).

vaa3d /x brainaligner /f brainaligner /p "#t   #s   #w <10>". I also ran into the same error when removing the <>.


-Brennan

"<>" is a parameters suggestions. You should run like 

vaa3d /x brainaligner /f brainaligner /p "#t #s #w 10".

Hope this helps.

Thanks,
Yang

Let me give you an example here:

Suppose you have a target image: target.tif
and target landmarks saved as: target.csv
and a subject image: subject.tif

1) global alignment;

./vaa3d /x brainaligner /f brainaligner /p "#t target.tif #s subject.tif #w 0 #o subject_ga.tif"

2) local alignment:

./vaa3d /x brainaligner /f brainaligner /p "#t target.tif #s subject_ga.tif #w 10 #o aligned_subject.tif #L target.csv"

The found corresponding landmarks in subject_ga.tif will be saved as csv file as well.

The brainaligner will efficient align your images but it might need you carefully pick control points to ensure your alignment meaningful. Good luck!

Best,
Yang

Thank you Yang for providing the example. Here is my result, same error. 

C:\Program Files\Vaa3D-3.20\bin>vaa3d /x brainaligner /f brainaligner /p "#t test1.tif #s test2.tif #o garesult.tif #w 0"
Qt: Untested Windows version 6.2 detected!
[vaa3d]
[/x]
[brainaligner]
[/f]
[brainaligner]
[/p]
[#t test1.tif #s test2.tif #o garesult.tif #w 0]
>>key ... /x
call plugin ... brainaligner
>>key ... /f
call plugin function ... brainaligner
>>key ... /p
Searching in ./plugins ......
Searching ./plugins done.
Current canonical path = [brainaligner]
Searching in ./plugins ......
Searching ./plugins done.
plugins
callPluginFunc fullpath: "C:/Program Files/Vaa3D-3.20/bin/plugins/image_registration/brainaligner/brainaligner.dll"
You have not specified the subject image or the output image. Do nothing.
Fail to call plugin function.
**** the plugin preprocessing takes [ 171 milliseconds]

C:\Program Files\Vaa3D-3.20\bin>

Originally posted by Yang Yu:

Hi Yang,

I am running into a new issue where vaa3d crashes on execution of the brainaligner. I am assuming I am getting an error because of failed plugin instantiations, though I am not sure what is causing this issue. 

The error is posted below. None are for the brainaligner function. Any idea on how to fix these issues? Thank you!!




____________________________________________________________________________________________________________________
C:\Program Files\Vaa3D>vaa3d_msvc /x brainaligner /f brainaligner /p "#t test1.tif #s test2.tif #w 0 #o subjectimg.tif"
Qt: Untested Windows version 6.2 detected!
[vaa3d_msvc]
[/x]
[brainaligner]
[/f]
[brainaligner]
[/p]
[#t test1.tif #s test2.tif #w 0 #o subjectimg.tif]
>>key ... /x
call plugin ... brainaligner
>>key ... /f
call plugin function ... brainaligner
>>key ... /p
"C:/Program Files/Vaa3D"
Searching in ./plugins ......
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.lib"
Searching ./plugins done.
Current canonical path = [brainaligner]
"C:/Program Files/Vaa3D"
Searching in ./plugins ......
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/linker_file/Linker_File_Generator/linker_file_generator.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/misc/combine_file/combine_file.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_tracing/segment_maker/segment_maker.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc/pruning_swc.lib"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.exp' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.exp"
Fail instantiation( The file 'C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.lib' is not a valid Qt plugin. ): "C:/Program Files/Vaa3D/plugins/neuron_utilities/pruning_swc_simple/pruning_swc.lib"
Searching ./plugins done.
"C:/Program Files/Vaa3D"
plugins
callPluginFunc fullpath: "C:/Program Files/Vaa3D/plugins/image_registration/brainaligner/brainaligner.dll"

C:\Program Files\Vaa3D>

Is that because you were using Windows?

Another person just tested yesterday and obtained results which look pretty nice to me. I suspect your setup has some issue.....

-Hanchuan Peng

I tested brainalinger on windows yesterday, it works fine!
Although I also got "Fail instantiation" errors as you listed above, but they are not about brainaligner and seems they will not effect it. 

Since the program complains it can not find your images, maybe you can try to use the absolute path instead, below is paras I used. Hope this helps!

#global alignment
.\vaa3d_msvc.exe /x brainaligner /f brainaligner /p "#t d:\downsampled\mouse17545redl5_s2.v3draw #s d:\downsampled\mouse17302l5_s2.v3draw #w 0 #o d:\downsampled\mouse17302l5_s2_jba_global.tif"

#local alignment
.\vaa3d_msvc.exe /x brainaligner /f brainaligner /p "#t d:\downsampled\mouse17545redl5_s2.v3draw #s d:\downsampled\mouse17302l5_s2_jba_global.tif #w 10 #o d:\downsampled\mouse17302l5_s2_jba_local.tif"


-Lei

Hi Lei,

Thank you for testing the function. The error is definitely from my end, I am running into an error whenever I call this function (image attached). I re-installed the latest release, and tried also version 3.458 (though with 3.458 I don't receive the plugin errors). Which version are you currently using? 

Brennan