[nipype] spm fieldmap

[Juliane]

Hi all,

is there an interface for fieldmap correction with spm?

Thanks.

Juliane

[Satrajit Ghosh]

hi juliane,

presently we do not have such an interfaces. a contribution would be much welcome.

cheers,

satra

Juliane

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[Juliane]

I wrote an interface for creating the voxel displacement map and it works fine. But now I have a problem with the realign and unwarp function from spm. When I start running my interface I always get the same error:

130827-18:14:18,644 interface INFO:
     stdout 2013-08-27T18:14:18.644531:> In spm_jobman at 121
130827-18:14:18,644 interface INFO:
     stdout 2013-08-27T18:14:18.644531:  In pyscript_realignunwarp at 28
130827-18:14:19,51 interface INFO:
     stdout 2013-08-27T18:14:19.051026:Can not initialise realignunwarp: job is not a struct.
130827-18:14:19,114 interface INFO:
     stdout 2013-08-27T18:14:19.114189:
130827-18:14:19,114 interface INFO:
     stdout 2013-08-27T18:14:19.114189:
130827-18:14:19,114 interface INFO:
     stdout 2013-08-27T18:14:19.114189:------------------------------------------------------------------------
130827-18:14:19,114 interface INFO:
     stdout 2013-08-27T18:14:19.114189:Running job #1
130827-18:14:19,114 interface INFO:
     stdout 2013-08-27T18:14:19.114189:------------------------------------------------------------------------
130827-18:14:19,133 interface INFO:
     stdout 2013-08-27T18:14:19.133914:No executable modules, but still unresolved dependencies or incomplete module inputs.
130827-18:14:19,138 interface INFO:
     stdout 2013-08-27T18:14:19.138334:The following modules did not run:
130827-18:14:19,138 interface INFO:
     stdout 2013-08-27T18:14:19.138334:Skipped: Realign & Unwarp
130827-18:14:19,138 interface INFO:
     stdout 2013-08-27T18:14:19.138334:
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142146:MATLAB code threw an exception:
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142253:Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142253:------------------
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142253:Running job #1
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142253:------------------
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142253:
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:File:cfg_util.m
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Name:spm_jobman.m
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Line:112
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:File:yscript_realignunwarp.m
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Name:cfg_util
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Line:115
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:File:pm_jobman
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Name:pyscript_realignunwarp
130827-18:14:19,142 interface INFO:
     stderr 2013-08-27T18:14:19.142449:Line:835

Does anyone know what that means and how I can solve this? Thanks.

[Satrajit Ghosh]

hi juliane,

one way to debug this is to go to the working directory, edit the pyscript*.m file to remove the try catch statements and monitor in matlab why it fails.

i suspect that the error is related to this output:

stdout 2013-08-27T18:14:19.133914:No executable modules, but still unresolved dependencies or incomplete module inputs.

which suggests some other input needs to be there, but perhaps you can check the script to see if something is not being set. 

which version of matlab are you using?

cheers,

satra

[Satrajit Ghosh]

and which version of spm.

cheers,

satra

[David Meunier]

Hi Juliane,

I am running into the same problem as you, trying to use Nipype to reproduce some analyses conducted previously in SPM. Did you manage to implement the Realign & Unwarp SPM function as a Nipype node or function? If yes, would it be possible to have access to your code, maybe through a pull request? That would very helpful indeed.

Many thanks,

David Meunier

[Juliane]

Hi David,

I did not find the error in my realign & unwarp interface. I wrote an interface for the SPM function applyVDM and used this instead. But this interface I wrote could only be used with presubtracted phase and magnitude data because I had not enough time to implement the whole function in Nipype.

Juliane

[Chris Filo Gorgolewski]

Hi,

Could you share the interfaces you have written? Even if they are unfinished someone else (such as Stephan Howwol) can pick up where you left.

Best,

Chris

[René Küttner]

Hi Chris,

On Tuesday, December 10, 2013 2:25:20 PM UTC+1, Chris Filo Gorgolewski wrote:

Could you share the interfaces you have written? Even if they are unfinished someone else (such as Stephan Howwol) can pick up where you left.

Juliane is on vacation at the moment. However, I can tell you that we plan to share the interfaces soon.

  René

[Chris Filo Gorgolewski]

Fantastic - looking forward!

[Erik Kastman]

Sorry to drag up an old post, but did these SPM Fieldmap - Calculate / Apply VDM interfaces make it into a PR anywhere? Doesn't look like it from the github network and PR search. I'm happy to finish off a few simples ones if they're not complete. 

-Erik Kastman