Hey Lennart,

I get an error when running albo.

albo run -i 00hepoks_29 MR_Flair:00hepoks/29/flair_tra.nii.gz MR_T1:00hepoks/29/t1_sag_tfe.nii.gz

leads to

INFO: Resampling...
INFO: Skullstripping...
INFO: Biasfield correction...
INFO: Intensityrange standardization...
INFO: Extracting features...
INFO: Applying classifier...
INFO: Standardbrain registration...
Traceback (most recent call last):
File "/home/maier/.local/bin/albo", line 9, in
load_entry_point('Albo', 'console_scripts', 'albo')()
File "/home/maier/Workspacepython/albo/albo/init.py", line 26, in main
args.func(args)
File "/home/maier/Workspacepython/albo/albo/albo_run.py", line 51, in main
stdbrain_sequence, stdbrain_path)
File "/home/maier/Workspacepython/albo/albo/pipeline.py", line 57, in segment_case
auxilliary_transform=transforms[standardbrain_sequence])
File "/home/maier/Workspacepython/albo/albo/pipeline.py", line 257, in register_to_standardbrain
interp="nearestneighbour"
File "/home/maier/.local/lib/python2.7/site-packages/nipype/caching/memory.py", line 69, in call
interface.inputs.set(**kwargs)
File "/home/maier/.local/lib/python2.7/site-packages/traits/has_traits.py", line 1541, in trait_set
setattr( self, name, value )
File "/home/maier/.local/lib/python2.7/site-packages/nipype/interfaces/traits_extension.py", line 80, in validate
self.error( object, name, value )
File "/home/maier/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 172, in error
value )

traits.trait_errors.TraitError: The 'reference' trait of an ApplyXfmInputSpec instance must be an existing file name, but a value of '00hepoks/29/t1_sag_tfe.nii.gz' <type 'str'> was specified.`

But ls 00hepoks/29/t1_sag_tfe.nii.gz tells me that the file exists. Any idea what might cause this? Maybe the underscores in the filename?

With other files following the same naming schema I get the same error, but with the following not

albo run -i 00sisstest_36 MR_Flair:00sisstest/36/FLAIR.nii MR_T1:00sisstest/36/T1.nii

albo run -i 00hepoks_27 MR_Flair:00hepoks/27/flair_tra.nii.gz

albo run -i 00hepoks_27 MR_Flair:00hepoks/27/flair_tra.nii.gz MR_T2:00hepoks/27/t2_sag_tse.nii.gz

Is the T1 somehow treated differently than the T2 or FLAIR to MNI registration?