[Freesurfer] cortical thickess of brains from a 7T scaner with resolution 0.6*0.6*0.6
Dear expert, Our group have some data scaned from 7T scaner. I would like to calculate the cortical thickness of the data, however, when I processed them as I do for data from 3T scaner, I can not run recon-all command successfull to the end. Could you give me some suggestions on how to obtain the cortical thickness measure for the 7T data? Are there any parameters that I should chang when processing 7T data? Thanks a lot! Yuanchao ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS versions
Hi all, I am doing a study with FreeSurfer (80 subjetcs till now), and I have cases reconstructed with the versions 4.2 and 4.3. I want to continue the study, and install the 4.5 version. I saw that in this release the Destrieux Atlas was updated. Could i compare the cases from the versions 4.2, 4.3 and 4.5? Is it correct or I only should compare cases (volumes, thickness, ...) between the same version? Thanks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS versions
Hi Miguel, you are better off rerunning all your subjects with 4.5. It should keep all the manual interventions so it will just be machine time. cheers, Bruce On Mon, 14 Sep 2009, Jose Soares wrote: Hi all, I am doing a study with FreeSurfer (80 subjetcs till now), and I have cases reconstructed with the versions 4.2 and 4.3. I want to continue the study, and install the 4.5 version. I saw that in this release the Destrieux Atlas was updated. Could i compare the cases from the versions 4.2, 4.3 and 4.5? Is it correct or I only should compare cases (volumes, thickness, ...) between the same version? Thanks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selecting the best structural scan
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 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 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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Label sizes, min ROI size
Dear experts, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage surface). Following up on the recent post, I tried 'mris_curvature_stats' but it gives error if I dont specify the subject. I am not to familiar with different commands, perhaps there is another one that would work? 2) Is there any "golden standard" for the minimum p-value or minimum size of an ROI to be considered a significant finding? I expect this may differ quite a lot, depending on how strong the effects of a variable on cortical thickness can be expected. Still, if you could comment on this or refer me to some literature, I would be very grateful. Thank you a lot! Best regards, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Label sizes, min ROI size
Try something like this mri_segstats --slabel fsaverage lh path/to/lh.yourlabel.label --sum lh.yourlabel.sum The 4th column of the summary file will have the Area in mm^2 doug Agnieszka Burzynska wrote: > Dear experts, > I have 2 questions: > > 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got > statistics from these rois for each individual subject (by map-to-subjects, > etc.), but what I am now interested in is to know the size of the ROI on the > group level (so on the fsaverage surface). > > Following up on the recent post, I tried 'mris_curvature_stats' but it gives > error if I dont specify the subject. I am not to familiar with different > commands, perhaps there is another one that would work? > > 2) Is there any "golden standard" for the minimum p-value or minimum size of > an ROI to be considered a significant finding? I expect this may differ > quite a lot, depending on how strong the effects of a variable on cortical > thickness can be expected. Still, if you could comment on this or refer me > to some literature, I would be very grateful. > > Thank you a lot! > Best regards, > Aga > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help in Qdec
Hi All! Could anyone help me in 3 questions regarding Qdec and freesurfer? 1, I'd like to know what Curv does stand for? Because We have a highly significant difference in Curv among our groups unilaterally. 2. Is it possible to list the total brain volume for all my subjects? If so, how to do that. 3, And finally, could anyone cite an article where the processing steps of recon-all is described or mentioned. I need it for the methods, but i don't really know what happens to my data if i give the recon-all -autorecon-all command. Thank you very much for your help! Gergő ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
