Nipype: How to access ROIs thickness or volume from Freesurfer

nipype
freesurfer

#1

Hi,

Is there anyway to access the ROIs thickness and volume from Freesurfer Recon-all results using nipype?

Usually, I would run the command “aparcstat2table” and generate csv files from rh.aparc.stats and left.aparc.stats, and finally read they using pandas.

But now, I was trying to use mainly nipype interfaces. But I did not find an interface for this. Is there other way?

Best wishes,
Walter


#2

This isn’t the solution you’re looking for but why not wrap a regular python function that accomplishes that, as a Nipype function and plug that in your workflow? If you were already doing it with bash and the freesurfer command line tools, it shouldn’t be too onerous to do that with subprocess.call or subprocess.Popen

Though I don’t know if that command has already been wrapped, I guess the place to check is here:

https://nipype.readthedocs.io/en/1.1.4/interfaces/generated/interfaces.freesurfer.html