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LittleBrainLab / microbrain

Fully automated whole-brain diffusion MRI analysis of grey matter
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cortical segmentation (dev branch) #4

Open peter-mri opened 2 years ago

peter-mri commented 2 years ago

When running dev branch of MicroBrain, with input switches -b [0,1000] --dnlsam --eddy_cuda --microbrain-mask --mbrain-seg --mbrain-cort --cpu-num=24

it crashes with an error: Traceback (most recent call last): File "microbrain.py", line 530, in main(sys.argv[1:]) File "microbrain.py", line 515, in main tmp_freesurf_subdir = os.environ['SUBJECTSDIR'] + '/MBRAIN' + subID + '/' File "/usr/lib/python3.8/os.py", line 675, in getitem raise KeyError(key) from None KeyError: 'SUBJECTS_DIR'

output folders "registration" and "subcortical_segmentation" exist and seem to have bunch of folders/files in them.

grahamlittlephd commented 2 years ago

Is the environment variable SUBJECTS_DIR set in your terminal for FreeSurfer? Microbrain will also need read/write access to that folder, because it does some processing in there

peter-mri commented 2 years ago

Good call, I did set it up once, but didn't have it in .bashrc file and have restarted since. I wonder if it would be better to have your code actually set SUBJECTS_DIR for each dataset... The default freesurfer SUBJECTS_DIR is usually under /usr/local and is (and should be) read-only.