Hello everyone, I’m a Bio-Informatics student from The Netherlands and for a school project I’m using the Nipype afni interface. I’m trying to perform normalization on structural coregistrated images using the autoTLRC function in nipype based on the @auto_tlrc from Afni. Now I’m running into an error while running it, I’m very new to the neurology preprocessing field.
The error is the following:
‘/Users/erichoekstra/PycharmProjects/brainnetworks_eric_linda/structural_flirt+tlrc.HEAD’ <class ‘str’> was specified
It’s a FileNotFoundError, this file is indeed not in the folder stated above, but why is this not the case? Shouldn’t it be made by Afni?
My code in Python:
autoTLRC = afni.AutoTLRC() autoTLRC.inputs.in_file = 'structural_flirt.nii.gz' autoTLRC.inputs.no_ss = True autoTLRC.inputs.base = "MNI_avg152T1+tlrc" autoTLRC.cmdline '@auto_tlrc -base TT_N27+tlrc -input structural.nii -no_ss' res = autoTLRC.run()
Thank you in advance!