Dear Ursula,
is this from within a script? If so, can you please turn on execution tracing to check that it really expands to what you expect it to?
Jesper
On 26 Jan 2015, at 15:47, Úrsula Pérez <[log in to unmask]> wrote:
KInd RegardsHi Matthew,Yes, both exist.
2015-01-26 16:18 GMT+01:00 Matthew Webster <[log in to unmask]>:
Can you confirm both your input files exist ( ${anat_dir}/anatomic_ss.nii.gz and ${anat_dir}/anatomic.nii.gz )?
Kind RegardsMatthew
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:
Thank you very much,How can I solve it? I get the error in fnirt even when I only write the parameters --in and --aff.I have checked all the paths and files, but I get the error: "the file or folder do not exist".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.
Úrsula