Step by step breakdown .nii files?

#1

Hey all, I’ve located the slice timing .nii in the working directory, I was wondering if there’s a similar file somewhere for once the script finishes motion correction. I looked in the _hmc_wf folder but only see a .nii.mat and .nii.par… I was hoping to compare the scripts output directly after it completes motion correction to my old protocol directly after motion correction.

Thanks again for all the help!

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#2

This looks like it’s probably fMRIPrep related.

We currently use MCFLIRT, but do not use the output image, as we apply HMC transforms along with SDC and coregistration (as well as normalization for the MNI output space). In order to save space, nipype removes outputs of processes that are not passed along to other nodes in the workflow. You can adjust this by setting the remove_unnecessary_outputs parameter to false. For exaple, suppose you have a nipype.cfg file:

[execution]
remove_unnecessary_outputs = false

With fmriprep-docker, you can add --config nipype.cfg to your command line, and it will make sure that the file remains. If you’re not using Docker, then you should make sure this file is in your current working directory, for whatever your environment is.

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#3

Awesome, thanks! I’ll try this now

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#4

So far, it seems like I’m getting the same exact output as before… I am running it with singularity so I placed a file called “nipype.cfg” into my “workDir” folder (the one that spits out all the _wf folders at the end). I didn’t change my command to run singularity at all, I assumed from your explanation that it would automatically search the workingDirectory folder for config files. Am I understanding you correctly?

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#5

If you’re using singularity, the nipype.cfg should be in your current working directory (i.e. the directory that your script is run from) or in $HOME/.nipype.

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#6

Trying it now, fingers crossed

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