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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