Can you confirm both your input files exist ( ${anat_dir}/anatomic_ss.nii.gz and ${anat_dir}/anatomic.nii.gz )?

Kind Regards

Matthew

Hi,

the code is:

flirt -in ${anat_dir}/anatomic_ss -ref ${template} -out ${anat_dir}/anatomic_2std -omat ${anat_dir}/my_affine_transf.mat
fnirt --in=${anat_dir}/anatomic --aff=${anat_dir}/my_affine_transf.mat --cout=${anat_dir}/my_nonlinear_transf --config=$HOME/${desktopFolder}/Vicente/rs-fMRI/fnirt_config.cnf
applywarp --ref=$template --in=${anat_dir}/anatomic --warp=my_nonlinear_transf --out=${anat_dir}/my_warped_structural

I get the error at 2) fnirt

Thanks,

Úrsula

2015-01-26 15:22 GMT+01:00 Bryson Dietz <[log in to unmask]>:

Can you paste how your calling FLIRT and FNIRT? This can better help us help you. At what point do you get the error (1, 2, or 3)?

On Mon, Jan 26, 2015 at 7:54 AM, Úrsula Pérez <[log in to unmask]> wrote:

Hi all,

I'm trying to use fnirt to register an anatomical image to a standard template, no MNI152. I have modified the "Example Uses" from the FNIRT UserGuide ( 1)flirt, 2)fnirt and 3)applywarp ), and created a new .cnf file.

I have checked all the paths and files, but I get the error: "the file or folder do not exist".

How can I solve it? I get the error in fnirt even when I only write the parameters --in and --aff.

Thank you very much,

Úrsula