Strange Error: align_epi_anat.py

AFNI Message Board
1

During preprocessing AFNI crashes (seems like it can’t find the python directory) but this error only occurs for a handful of our subjects. What might be the source of the problem and why is it not a consistent issue? Any input would be great appreciated.

3dbucket -prefix vr_base pb02.s8.r01.tshift+orig[2]
++ 3dbucket: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
align_epi_anat.py -anat2epi -anat t1_MPRAGE+orig -save_skullstrip -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -AddEdge -volreg off -tshift off
/usr/bin/env: ‘python’: No such file or directory

2

That actually suggests ‘python’ is not in your PATH. Is that possible?

  • rick
3

I don’t think that is the case I can talk to our system administrator but first I will try to run these subjects again. The strangest thing is that things ran fine for some subjects and not others. I don’t know how the python path could temporarily disappeared.

4

It is hard to guess how that might be happening, but it does look like /usr/bin/env complaining that there is no ‘python’ to run.
That is the first line of align_epi_anat.py. Is this in the context of an afni_proc.py script?

  • rick
5

I’m new to AFNI and just installed it, but I’d like to add that I’m receiving a similar error: env: python: No such file or directory when using afni_proc.py and even afni_system_check.py. I think the issue may be that AFNI is looking for “python” when it should be looking for “python3”, because python3 is on usr/local/bin path in my case. Would appreciate any help

6

Howdy-

What is the output of:


afni_system_check.py -check_all

? Can you please copy+paste the text here.

-pt

7

env: python: No such file or directory

8

So, yes, it looks like you don’t have Python at all on your computer then. I have never really seen this before, because most operating systems come with at least some Python in the path, to be used.

What is the output of A):


lsb_release -a

and B)


echo $PATH

?

–pt

9

I have python on my computer, I know this because I installed it. The problem, I believe, is that it’s called “python3” and not “python”.

lsb_release -a lends command not found, I’m on a new Mac with M1.
Output of echo $PATH:

/opt/homebrew/bin:
/opt/homebrew/sbin:
/Library/Frameworks/Python.framework/Versions/3.10/bin:
/opt/homebrew/bin:
/opt/homebrew/sbin:
/usr/local/bin:
/usr/bin:
/bin:
/usr/sbin:
/sbin:
/opt/X11/bin:
/Users/me/abin

10

Consider installing miniconda to manage python and other software for you. On my M1 Mac, I do have python installed by default in /usr/bin. It’s version 2.7.18 on a Mac with 12.2.1 (Monterey) that is just a symbolic link to the system library framework version. The instructions are shown below for conda.

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/miniconda.html#install-miniconda

% which python
/Users/dglen/miniforge3/envs/py39_afni_tiny/bin/python
dglen@Brians-MacBook-Air python_scripts % conda
% where python
/Users/dglen/miniforge3/envs/py39_afni_tiny/bin/python
/usr/bin/python
% /usr/bin/python --version
Python 2.7.18
% ls -l /usr/bin/python
lrwxr-xr-x 1 root wheel 75 Feb 6 16:22 /usr/bin/python → …/…/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
% file /usr/bin/python
/usr/bin/python: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit executable x86_64] [arm64e:Mach-O 64-bit executable arm64e]
/usr/bin/python (for architecture x86_64): Mach-O 64-bit executable x86_64
/usr/bin/python (for architecture arm64e): Mach-O 64-bit executable arm64e

11

Solved, thank you!

12

What was your solution, may I ask?

Did you make your own symbolic link from /usr/local/bin/pyhton3 to /usr/local/bin/python?

This suggests that homebrew might not be putting any ‘python’ in the path dirs, but it is also strange for there to be no system python under /usr/bin.

To be sure:

  • What OS version are you running?
  • What it just view homebrew that you installed python?
  • Was anything special done for python in your case?

Thanks,

  • rick
13

Rick,

I did not create a symlink because I didn’t want to disable SIP on my Mac. I’m using Monterey 12.3, and I downloaded python3 using the installer from the python website; I didn’t do anything with homebrew other than what was required for setting up AFNI. I downloaded miniconda and created a conda environment for AFNI. I was able to run afni_system_check.py after activating this environment, as described here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html#setup-python-opt

Justin

14

Hi Rick,

I am sorry for the late reply my attention had to move away from this issue. I am using a Linux machine and I ran afni_system_check.py -check_all. I certainly have python on my machine. Below are excerpts from the output.

which python : /usr/bin/python
python version : 2.7.5

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/bin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)

15

Is there a context difference, meaning are you sometimes running under a conda environment?
One thing that is odd is that afni_system_check and align_epi_anat.py invoke python in exactly the same way. So it is curious that afni_system_check.py runs well, but align_epi_anat.py gives an error. There seems to be an environmental difference between how they are being run.

To be sure, what is the output from:

which python
python -V
/usr/bin/env python -V

And if you have a conda env, would you run the same commands from there?

Thanks,

  • rick