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. >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >> >>
euler_comparison.xls
Description: MS-Excel spreadsheet
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
