I have an experiment with 3 different sequences, but the maximum difference I've found was 5% ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

2009/9/4 sima chalavi sima.chalavi@gmail.com

Hi Pedro, Thanks for your reply,

Actually I am using 6 different sequences for scanning the same subject, so a small part of the difference could be because of randomness, but there should be a way to select the best scan from these 6 different scans. I need to know how to select the best.

any suggestion?

Regards, Sima.

2009/9/4 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br

...

Hi Sima, I've run 6 versions of the same scan of the same subject I got some differences too. Not so big as you found but still some differences

Probably it's the -randomness flag in the recon-all

Check: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html cheers

---

Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

2009/9/4 sima chalavi sima.chalavi@gmail.com

...

Dear Freesurfer experts,

We performed 6 different (pilot) structural scans from the same subject and analyzed the data using Freesurfer in order to find the best scan to be used in our real experiment.

We have checked the Freesurfer output visually and there do not seem to be any problem as described in the trouble shooting manual. So all 6 scans manage to get through the Freesurfer process just fine.

However, There are a lot of differences between the numerical results for the different scans. Please find Attached graphs of (some of ) the results of segmentation and parcellation of these 6 sequences from the statistical outputs. Now, the problem is how to select the best scan from these results.

Does any body have a standard protocol for assessing images for analysis or a standard metric, e.g. goodness of fit, from the software that we can assess without having a gold standard?

Or any other tip is also appreciated.

Thanks in advance,

Sima.