Hello,

I just wanted to follow up to note that I did a bit more digging, and compared the freesurfer log files on this new batch, versus that which was successfully run last August. There are no differences in terms of the log files, with the exception of course that additional people were run. I also completely re-ran everyone, and removed the old successfully run files to a back-up drive to be able to go from scratch, and have still not been able to generate the snapshots. ImageMagik and GNU awk are both up to date. Any suggestions?

Thanks,

Jessica

On Mon, Apr 21, 2014 at 10:52 AM, Jessica Bernard <jbernard21@gmail.com> wrote:

Hi All,

I've been running the Freesurfer QA Tools on some new data, and have been having some difficulties with the outputs. I am running this using the -snaps-detailed flag. In the past, we have had .html links, but also detailed .gif files for each person. We've consistently had trouble with the .html links, but the .gif files have been perfectly fine. However, when running new individuals, not only are the images broken in the .html output, but there are no gif files (which are preferred). Is there an additional command that needs to be added to generate the detailed gif files as well? Sorry if this is a rather basic question. I recently took over the Freesurfer QA process, and am relatively new to the functions, and my predecessor does not know how they created the gif files (the first batch of QA was run 6 months ago with our first wave of data collection). Thanks in advance for any help you may be able to provide.

Best Wishes,
Jessica