[nipype] sprint irc channel

[Satrajit Ghosh]

#nipype on freenode

cheers,

satra

[Horea Christian]

I couldn't find this - has it been discontinued?

[Satrajit Ghosh]

hi christian,

we are over at: https://gitter.im/nipy/nipype/~chat#initial

cheers,

satra

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[matthew garlinghouse]

Hello listmates,

Beginning to explore nipype - really enjoying the flexibility it offers.  Am building a pipeline that includes attempting to use ANTS matrix file as input to the spmu.ApplyTransform - not sure SPM will be able to read that anyway, but regardless I will find out  :)..

However before I am able to error out SPM, I get the following Matlab error:

######################################################

Executing pyscript_applytransform at 26-Sep-2014 17:04:34:
--------------------------------------------------------------------------------------------------------
MATLAB Version: 8.0.0.783 (R2012b)
MATLAB License Number: 909935
Operating System: Mac OS X  Version: 10.8.5 Build: 12F45
Java Version: Java 1.6.0_65-b14-462-11M4609 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
--------------------------------------------------------------------------------------------------------
MATLAB                                                Version 8.0        (R2012b)
Image Processing Toolbox                              Version 8.1        (R2012b)
Statistical Parametric Mapping                        Version 5236       (SPM8) 
Statistics Toolbox                                    Version 8.1        (R2012b)
Template-O-Matic Toolbox                              Version 9          (TOM8) 
Voxel Based Morphometry Toolbox                       Version 435        (VBM8) 

Standard error:
MATLAB code threw an exception:
Reference to non-existent field 'M'.
File:/Users/ccnc/Desktop/For_MG/script_test/G1/firstlevel/level1pipeline/_subject_id_Sub_001_grp1/xfm/pyscript_applytransform.m
Name:pyscript_applytransform
Line:6

Return code: 0
Interface MatlabCommand failed to run.
Interface ApplyTransform failed to run.

######################################################

I believe it is related to the following line in the pyscript code, "M = inv(transform.M);"


Thoughts?

Best,

Matthew

[Satrajit Ghosh]

hi matthew,

unfortunately SPM cannot handle anything other than it's own transformations. so you will have to figure out how to do the appropriate conversion from the itk format to a matlab matrix which spm can use. 

cheers,

satra

[matthew garlinghouse]

Hello Satrajit,

I should have known  ;)..

OK, I will work on that.  In the mean time I have opted to use spm.calccoregaffine to generate and pass along the matrix file to spm.applytransform. 

However I am getting the following error:

#######################################
Executing pyscript_calccoregaffine at 29-Sep-2014 09:32:17:

--------------------------------------------------------------------------------------------------------
MATLAB Version: 8.0.0.783 (R2012b)
MATLAB License Number: 909935
Operating System: Mac OS X  Version: 10.8.5 Build: 12F45
Java Version: Java 1.6.0_65-b14-462-11M4609 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
--------------------------------------------------------------------------------------------------------
MATLAB                                                Version 8.0        (R2012b)
Image Processing Toolbox                              Version 8.1        (R2012b)
Statistical Parametric Mapping                        Version 5236       (SPM8) 
Statistics Toolbox                                    Version 8.1        (R2012b)
Template-O-Matic Toolbox                              Version 9          (TOM8) 
Voxel Based Morphometry Toolbox                       Version 435        (VBM8) 

Standard error:
MATLAB code threw an exception:

Too many input arguments.
File:/Applications/spm8/spm_coreg.m
Name:/Applications/spm8/spm_coreg.m
Line:47
File:Users/ccnc/Desktop/For_MG/script_test/G1/firstlevel/level1pipeline/_subject_id_Sub_001_grp1/coregister/pyscript_calccoregaffine.m
Name:loaduint8
Line:115
File:pm_coreg
Name:pyscript_calccoregaffine
Line:222
File:y
Name:
Line:

Return code: 0
Interface MatlabCommand failed to run.

Interface CalcCoregAffine failed to run.

########################################

Sorry to bother about this.  Generally I have relatively good luck sorting through these sorts of things, but this one has had me stumped for a bit. 

Thoughts?

Kind Regards,

Matthew

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