Hello FreeSurfer Developers,

I am having some problems using the mri_cvs_register toolbox of FS.

The error is the following one (it is caused even in the simplest case of registration of the sample data file "$FREESURFER_HOME/subjects/sample-001.mgz" over the CVS template)(the installation folder is /home/zappst/Desktop/freesurfer):

zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs

Log file is /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log

/home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log: No such file or directory.

Then I tried to add the "--nolog" argument, causing another error:

zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz --nolog Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs sLF: Undefined variable.

Actually, the same error regarding the undefined variable sLF is caused even when calling mri_cvs_register on other images.

I tried in vain to uninstall FS and now I have the version "freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0" on Ubuntu 16.04 LTS. The test reported in http://freesurfer.net/fswiki/DownloadAndInstall for testing the installation completed successfully (so it seems that the problem is related to mri_cvs_register).

So, I was wondering what can I do in order to solve the problem.

Thanks for the attention.

Best, Stefano.