命令可以从Shell脚本运行，但不能从命令行运行？

Question

I quickly searched for this before posting, but could not find any similar posts. Let me know if they exist.

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The commands being executed seem very simple. A directory listing is used as the input for a function.

The directory contains a bunch of files named "epi1_mcf_0###.nii.gz"

Command-line version (bash is running when this is executed):

fslmerge -t output_file `ls epi1_mcf_0*.nii.gz`

Shell script version:

#!/bin/bash
fslmerge -t output_file `ls epi1_mcf_0*.nii.gz`

The command-line version fails, but the shell script one works perfectly.

The error message is specific to the function, but it's included anyway.

** ERROR (nifti_image_read): failed to find header file for 'epi1_mcf_0000.nii.gz'
** ERROR: nifti_image_open(epi1_mcf_0000.nii.gz): bad header info
Error: failed to open file epi1_mcf_0000.nii.gz
Cannot open volume epi1_mcf_0000.nii.gz for reading!

I have been very frustrated with this problem (less so after I figured out that there was a way to get the command to work).

Any help would be appreciated.

(Or is the general consensus that the problem should be looked for in the "fslmerge" function?)

Answer 1

`ls epi1_mcf_0*.nii.gz` is better written as simply epi1_mcf_0*.nii.gz . As in:

fslmerge -t output_file epi1_mcf_0*.nii.gz

The `ls` doesn't add anything.

^{Note: Posted as an answer instead of comment. The Markdown-lite comment parser choked on my `` `ls epi1_mcf_0*.nii.gz` `` markup.}

Answer 2

(I mentioned this in a comment first, but I'll make an answer since it helped!)

Do you have any shell aliases defined? (Type alias ) Those will affect commands typed at the command line, but not scripts.

Linux often has ls defined as ls --color . This may affect the output since the colour codes are sent as escape codes through the regular output stream. If you use ls --color=auto it will auto-detect whether its output is a terminal or not. From man ls :

By default, color is not used to distinguish types of files. That is equivalent to using --color=none . Using the --color option without the optional WHEN argument is equivalent to using --color=always . With --color=auto , color codes are output only if standard output is connected to a terminal (tty).