Satrajit Ghosh

that should help. there is an error that is cropping up in doctests because nipype is printing out a message. this could be avoided by importing nipype earlier. but i...

this is because the first time nipype is imported in a terminal interaction setting, it will try to check if you are running the latest version. this results in a...

you can use the standalone version of SPM. some details here: https://miykael.github.io/nipype_tutorial/notebooks/advanced_spmmcr.html

you may want to use absolute path here for `spm12/run_spm12.sh`: ``` spm.SPMCommand.set_mlab_paths(matlab_cmd='spm12/run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ script', use_mcr=True) ```

just a note that we may have to do something different between SPM12 and prior versions. in pre SPM12, orth was sequential and order mattered (and interpretation mattered). this was...

@hstojic - that particular error is because for some reason it cannot determine spm version: `self.version`

every measure that's in the header of aseg.stats + corpus callosum + ventricular stats. i don't think the latter two are present in the current output. ``` # Measure BrainSeg,...

run asegstats2table returns a list of specific subcortical and whole brain stats for a subject. i would suggest including those only.

> asegstats2table --subjects bert needs python2, not updated yet to use python 3 ( there is a version in their dev repo which would likely run on python3, but the...

given the python situation it would be best to perhaps just parse the aseg.stats directly using pandas.