Hi Farras Try replacing "~" by the interpreted version (i.e. the path to your home directory). Cheers, Saad On 4 Jan 2012, at 18:00, Farras Abdelnour wrote: > Dear everyone, > I am a fairly new user of FSL, and trying to run the command probtrackx from within Matlab. I use the following command: > > system(sprintf('probtrackx --mode=seedmask -x %s -l -c 0.2 -S 2000 --steplength=0.5 -P %d --xfm=%s --stop=%s --forcedir --opd -s %s -m %s --dir=%s',src_mask,num_samples,standard2diff_out_mat,tar_mask,bedpostx_merged,nodif_brain_mask,out_dir)); > > and get the following message: > > ** ERROR (nifti_image_read): failed to find header file for '~/Documents/fMRI_data/17-R-subject4/e006443/DTI/fsl_dti/masks/target_mask_001' > ** ERROR: nifti_image_open(~/Documents/fMRI_data/17-R-subject4/e006443/DTI/fsl_dti/masks/target_mask_001): bad header info > ERROR: failed to open file ~/Documents/fMRI_data/17-R-subject4/e006443/DTI/fsl_dti/masks/target_mask_001 > ERROR: Could not open image ~/Documents/fMRI_data/17-R-subject4/e006443/DTI/fsl_dti/masks/target_mask_001 > Image Exception : #22 :: Failed to read volume ~/Documents/fMRI_data/17-R-subject4/e006443/DTI/fsl_dti/masks/target_mask_001.nii > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > > Has anyone encountered a similar issue? Any help would be most appreciated. > -- > Farras Abdelnour > http://sacklerinstitute.academia.edu/FarrasAbdelnour > Imaging Data Evaluation and Analytics Laboratory (IDEAL) > Department of Radiology | Weill Cornell Medical College > 515 E. 71st St., S-125 | New York, NY 10065 > email: [log in to unmask] > http://ideal-cornell.com -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad