On 11/04/2016 07:30 AM, anonymous anonymous wrote:

Hi all,

I'm new to freesurfer and I'm having some issues.

1. First of all I tried recon-all in one subject but I got an error on

nu_correct. This is what the log says:

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct

This is a known issue due to an incompatibility between the mni tools shipped with freesurfer 5.3 and the version of perl shipped with ubuntu 16. The issue is fixed in the upcoming release of freesurfer v6, but in the meantime the only known solution is to download and install the development version of freesurfer, available from the page (see "Development Version"):

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

I searched through the mail list and I found that it may be because my data is in an external hard drive... (the hard drive is in FAT32). But it's not because the data is in the external hard drive. I copied a folder to my computer and I got the same problem. Could it be the data?

2. Then I tried to install CUDA 8.0 ... I don't know if succesfully

because the command cudadetect shows the following:

cudadetect.bin: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory

Reading as well I'm afraid that freesurfer may not be able to use versions of CUDA that are +5? I have an NVIDIA Geforce GTX 950 and using NVIDIA binary driver version 370.28.

Freesurfer was compiled against cuda5, so you'll need that version, which admittedly is fairly ancient at this point. Its unlikely to change in the future because we no longer actively support cuda, as we've focused our efforts on openmp.

3. I think after the installation of CUDA using a .deb I got the paths

messed up and now I can't even use recon-all on my hard drive. When I type recon-all on any other external hard drive or folder, it does show the information though. I dont know if it's a permissions problem (I also had a blackout earlier...) but the hard disk's files and folders seem to have all permissions and the ownership is root:root. I can't remount it now because I'm running some things using fsl...

Not sure how to help with this other than to add the location of recon-all (which is installed in $FREESURFER_HOME/bin, usually /usr/local/freesurfer/bin) to your PATH environment variable.

Please any help would be really appreciated. I've spent a loooot of hours struggling with all these.

I'm on a ubuntu 16.04 by the way.

Thaaaaaankius

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