Hi Sima,
you should also make sure that the surfaces are visually accurate (that
is, the white and pial surfaces lie at the true boundaries). If that's the
case then either 03 or one of the 05s is the next best. For the
distributions, you can use the aparc+aseg.mgz to extract the correct voxel
indices in matlab, then plot the distributions of the norm.mgz with hist.
cheers
Bruce
On Tue, 15 Sep
2009, sima chalavi wrote:
Dear Bruce,
Thanks so much for your email,
I ran mris_euler_number and mri_cnr (see attachment) according to your
advice, it is already clear for us to remove G02 because of having too small
Euler number. It is also clear that for this particular scanner the G05_H_11
sequence is the best.
For our multi-centre study we want to test more than one sequence on the
next scanner. Therefore, for selecting a second best scan, I need to do
further analysis. I want to test your suggestion about checking intensity
distribution.
I was wondering how I retrieve the intensity values you suggested to be able
to plot the intensity distribution. Secondly we were wondering how to decide
the (second) best scan checking that?
Thank you again for all your help,
Sima.
2009/9/14 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Hi Sima,
it's hard to say just from the tiffs. A couple of things you can look at:
run mris_euler_number on the lh.orig.nofix and the rh.orig.nofix. Better
sequences should result in bigger (less negative) euler numbers.
Plot the intensity distributions of the gray matter, CSF and the white
matter as histograms and see how much they overlap and how broad they are.
Use mri_cnr to compute the gray/white CNR from the surfaces.
cheers,
Bruce
On Mon, 14 Sep 2009, sima chalavi wrote:
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 <fis...@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 <p...@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.chal...@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.
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