Hi Xinman,
You have two problems:
1. Your files are called *.nii, not *.nii.gz. So the correct
tbss_1_preproc command
to use is:
tbss_1_preproc *.nii
2. Your system appears to be missing some libraries required by FSL.
What operating
system are you using?
Paul
On 08/05/2019, Xinman Liu <[log in to unmask]> wrote:
> Hi, Paul.
> Thank you for your quick reply.
> I used FSL 6.0.1 version, and I believe the installation completed
> successfully. And after tbss_1_preproc *.nii.gz. It creates two folder named
> FA and origdata, but unfortunately there's nothing in it, and the nii
> documents are outside these two files. And I knew that they actually should
> be all in the file named origdata. But when I used tbss_1_preproc *.nii,
> something different happened. It still creates the same two folder named FA
> and origdata. There is target.nii.gz and tbss_logs in FA, and the original
> data are now in origdata file. But when I type in tbss_2_reg -T, the result
> is still the same. What do you think should be the problem?
>
> [fsluser@localhost ~]$ cd mytbss
> [fsluser@localhost mytbss]$ ls
> a_fa.nii d_fa.nii g_fa.nii j_fa.nii m_fa.nii P_fa.nii s_fa.nii
> b_fa.nii e_fa.nii h_fa.nii k_fa.nii n_fa.nii q_fa.nii t_fa.nii
> c_fa.nii f_fa.nii i_fa.nii l_fa.nii o_fa.nii r_fa.nii
> [fsluser@localhost mytbss]$ tbss_1_preproc *.nii.gz
> Now running "slicesdir" to generate report of all input images
> -e <thr> : use the specified threshold for edges (if >0 use this
> proportion of max-min, if <0, use the absolute value)
> -S : output every second axial slice rather than just 9 ortho
> slices
> [fsluser@localhost mytbss]$ ls
> a_fa.nii d_fa.nii f_fa.nii i_fa.nii l_fa.nii o_fa.nii q_fa.nii
> t_fa.nii
> b_fa.nii e_fa.nii g_fa.nii j_fa.nii m_fa.nii origdata r_fa.nii
> c_fa.nii FA h_fa.nii k_fa.nii n_fa.nii P_fa.nii s_fa.nii
> [fsluser@localhost mytbss]$ cd FA
> [fsluser@localhost FA]$ ls
> [fsluser@localhost FA]$ cd ..
> [fsluser@localhost mytbss]$ cd origdata
> [fsluser@localhost origdata]$ ls
> [fsluser@localhost origdata]$[fsluser@localhost origdata]$ cd ..
>
> [fsluser@localhost mytbss]$ tbss_2_reg -T
> Task file (.commands) does not exist
> [fsluser@localhost mytbss]$ ls
> a_fa.nii d_fa.nii f_fa.nii i_fa.nii l_fa.nii o_fa.nii q_fa.nii
> t_fa.nii
> b_fa.nii e_fa.nii g_fa.nii j_fa.nii m_fa.nii origdata r_fa.nii
> c_fa.nii FA h_fa.nii k_fa.nii n_fa.nii P_fa.nii s_fa.nii
>
>
> [fsluser@localhost mytbss]$ tbss_1_preproc *.nii
> processing P_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing a_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing b_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing c_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing d_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing e_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing f_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing g_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing h_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing i_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing j_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing k_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing l_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing m_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing n_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing o_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing q_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing r_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing s_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> processing t_fa
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslhd: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> dc: stack empty
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> /usr/local/fsl/bin/fslmaths: error while loading shared libraries:
> libquadmath.so.0: cannot open shared object file: No such file or directory
> Now running "slicesdir" to generate report of all input images
> -e <thr> : use the specified threshold for edges (if >0 use this
> proportion of max-min, if <0, use the absolute value)
> -S : output every second axial slice rather than just 9 ortho
> slices
> [fsluser@localhost mytbss]$ ls
> FA origdata
> [fsluser@localhost mytbss]$ cd FA
> [fsluser@localhost FA]$ ls
> target.nii.gz tbss_logs
> [fsluser@localhost FA]$ cd ..
> [fsluser@localhost mytbss]$ cd origdata
> [fsluser@localhost origdata]$ ls
> a_fa.nii.gz e_fa.nii.gz i_fa.nii.gz m_fa.nii.gz q_fa.nii.gz
> b_fa.nii.gz f_fa.nii.gz j_fa.nii.gz n_fa.nii.gz r_fa.nii.gz
> c_fa.nii.gz g_fa.nii.gz k_fa.nii.gz o_fa.nii.gz s_fa.nii.gz
> d_fa.nii.gz h_fa.nii.gz l_fa.nii.gz P_fa.nii.gz t_fa.nii.gz
> [fsluser@localhost origdata]$ cd ..
> [fsluser@localhost mytbss]$ tbss_2_reg -T
> Task file (.commands) does not exist
>
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