Hello, I’m yahya and I’m new to this forum.
I tried to run the mne-biomag-group-demo on COLAB but I faced some issues by running the file 01-anatomy.py where they asked to install FreeSurfer first. I installed it but now my problem is that how can i use this FreeSurfer in Colab because after installing I got the same error.
The error is :
Processing sub001
Running reconstruction (usually takes hours)
Running :
recon-all -all -s sub001 -sd /content/gdrive/MyDrive/mne-biomag-group-demo/scripts/processing/library/…/…/…/subjects -i /content/gdrive/MyDrive/mne-biomag-group-demo/scripts/processing/library/…/…/…/ds117/sub001/anatomy/highres001.nii.gz
Traceback (most recent call last):
File “01-anatomy.py”, line 139, in
parallel(run_func(subject_id) for subject_id in range(1, 20))
File “01-anatomy.py”, line 139, in
parallel(run_func(subject_id) for subject_id in range(1, 20))
File “01-anatomy.py”, line 61, in process_subject_anat
‘-i’, t1_fname], log_fname)
File “01-anatomy.py”, line 38, in tee_output
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
File “/usr/lib/python3.7/subprocess.py”, line 800, in init
restore_signals, start_new_session)
File “/usr/lib/python3.7/subprocess.py”, line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘recon-all’: ‘recon-all’