Dear Bruce,

Thank you for this advice. We understand the importance of
optimalising the proposed factors. Do you perhaps have tips on
programs that we can use to assess these factors?

In addition, we are wondering how the factors influence the output of
Freesurfer. For example, if we optimize the contrast-to-noise how will
this effect the cortical thickness measure? The reason for this question is depicted in the attachments. We have compared our sequences to 'bert', lined up in talairach space. Which sequence would you prefer on the basis of visual inspection?

Thanks you again for your help,
 Sima.

2009/9/4 Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Hi Sima,

you could compute the contrast-to-noise ratio between gray and white, which will give you some idea. The overall optimization is very difficult though as there are factors like distortion, contrast uniformity, etc....

cheers
Bruce

On Fri, 4 Sep 2009, sima chalavi wrote:

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.