title: Issues running FSL command in Linux environment
body: <p>I am new to FSL, using version 4.1.8. I am trying to run a script that reads and generates <code>*.nii</code> files, which format is normally supported by FSL. I am calling an FSL function, <code>probtrackx</code> from within <code>Matlab</code>. However, I get the following error message seemingly unable to generate or recognize <code>*.nii</code> files:</p>
  
  <pre><code>** ERROR (nifti_image_read): failed to find header file for '~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001'
  
  ** ERROR: nifti_image_open(~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001): bad header info
  
  ERROR: failed to open file ~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001
  
  ERROR: Could not open image ~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001
  </code></pre>
  
  <p>The files do exist but FSL fails to recognize them. Any help as to how to correct the issue and get FSL to work properly would be most appreciated. I suspect it's a Linux settings issue, just not sure how to fix it. A solution to a related problem in a previous posting suggested adding <code>ls='ls --color=auto'</code>. I've tried it to on avail.</p>