got some problem when execute freesurfer command by anaconda

[MaJie414]

No description provided.

[MaJie414]

`import subprocess
def tee_output(command, log_file):
"""Write the output of a command to a logfile as well as stdout."""
print('Writing the output of the command below to', log_file)
print(' '.join(command))
with open(log_file, 'wb') as fid:
proc = subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
for line in proc.stdout:
fid.write(line)
if proc.wait() != 0:
raise RuntimeError('Command failed')

subject = 'dd'
tee_output(['recon-all', '-all', '-s', subject, '-sd', '/media/mj/D/sharefolder/Linux_soft/freesurfer/subjects',
'-i', '/home/mj/Downloads/rT1.nii'],
'dd.txt')
`
My code is here.
I got an error when executing this code.

[wmvanvliet]

You don't have freesurfer installed.

[MaJie414]

I already have installed the freesurfer. It's work when I copy the command(recon-all -all -s dd -i /home/mj/Downloads/rT1.nii) to shell window. But it couldn't execute by python, even using os.system() still report an error.

[wmvanvliet]

if it works if you cope/paste the command in your terminal, then it must be a path issue. Is your python somehow using a different $PATH environment variable? Can you try editing the code of the script to contain the full path to the recon-all program?