Dear Ana,
It looks like you have a very old version of FSL.
I recommend updating to the latest version and then running FIRST.
The syntax that your version is asking for is very out of date, which
is why it is different from the online documentation.
All the best,
Mark
On 8 Jul 2011, at 22:58, Ana Arruda wrote:
> Hello,
>
> I'm a MSc student and for my final project I have to learn how to measure the volume of hippocampus using the automatic segmentation. Although I've been working with FSL, more specifically with FIRST and some doubts appeared. Like it is said in the website I thought that I have to write in the X11 terminal run_first_all -i t1_image -o output_name but when I write that appears run_first_all <input_image> <boundary_threshold> <output>. I don't know what does the insert number in "boundary_threshold" mean and if it's always generated many files like "clean_up.e6846.1", "clean_up.o6846.1", "input_name_to_std.mat", "input_name_to_std_nii.gz", ".vtk", ".bvars", "first.e" and "first.o".
>
> Sorry for this mess and thank you for your attention.
>
> Ana
>
|