Re: [Freesurfer] Fwd: selecting the best structural scan
Along the same vein, I found this page on the freesurfer site: http://surfer.nmr.mgh.harvard.edu/fswiki/QATools but it doesn't seem to link to any actual tools? have these been discontinued? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Sep 4, 2009, at 4:03 AM, sima chalavi wrote: 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. -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com six_structural_statistics.pdf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: selecting the best structural scan
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. -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: selecting the best structural scan
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.chal...@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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
