Hi Megan:
I'm much less of an expert than Cyril, but I spend a fair bit of my time building batches that loop over many subjects.
A few things I have found helpful in troubleshooting and learning the intricacies of the batch system is:
1. Create a single subject job that runs well. Take a close look at all the variables in MATLAB and actually open all the variables. This will help you figure out exactly what kind of arrays the batch is expecting -- this is often the problem when your input variables aren't working.
2. Run your test batch file section by section in MATLAB - this can help figure out where things are getting stuck
3. Take a close look at the spm_jobman code sections
4. Set up a loop script and data structure that automagically interface with matlabbatch via jobman. This will help give you input fields correctly specified for your various inputs to whatever batch modules you're setting up (and also not have to recreate the wheel every time)
I don't use spm for DICOM conversion (I use dcm2niix directly which works very nicely - if you want to check that out you can get MRICroGL) but just guessing, it sounds like maybe the batch system is looking for you to use one of the directory or file selector modules to create dependencies for the conversion module.
Best
Nina
On Sun, 16 Oct 2016, PERNET Cyril wrote:
> Hi Megan,
>
> Check inside spm subfolders (can't remember which one) there are a few working batch exemples
>
> Best
> Cyril
>
> ----- Reply message -----
> From: "Megan Finnegan" <[log in to unmask]>
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: [SPM] Using SPM12 generated batch scripts
> Date: Sun, Oct 16, 2016 19:10
>
> Hello,
> SPM newbie here, wondering if anyone could share a working example of (or otherwise explain) how to use the batch files that can be generated by the SPM GUI?
>
> Right now I'm trying out a toy example of dicom import looping over multiple subjects. When I create a loop and specify the relevant files directly in the created job file it runs beautifully, but
> when I try to populate the inputs variable created within the generated batch main script using this same values I get an unresolved dependency error.
>
> After poking around a bit, it seems that the job is not getting populated with the inputs data. Is there an alternate format that the data should be specified in the inputs variable that is
> different from the format needed for the job file? What am I doing wrong?
>
> Thank you for any help you can provide!
>
> Regards,
> Megan
>
>
>
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