From Li.Su at mrc-cbu.cam.ac.uk Tue Nov 9 11:59:00 2010 From: Li.Su at mrc-cbu.cam.ac.uk (Li Su) Date: Tue, 9 Nov 2010 16:59:00 +0000 Subject: [Mne_analysis] Changing EEG electrodes coordinates In-Reply-To: <31166.155.52.176.37.1277220691.squirrel@mail.nmr.mgh.harvard.edu> References: <31166.155.52.176.37.1277220691.squirrel@mail.nmr.mgh.harvard.edu> Message-ID: Dear MNE users, I would like to convert a 3D STC structure to a 2D matrix in Matlab which represents the flattened brain. It doesn't matter too much if I lose some areas of the brain, e.g. the medial wall, or the 2D map is slightly distorted. Apparently, MNE can visualise this, but it is not clear to me if I can export the 2D map to Matlab. Many thanks for your help, Li Su -- Li Su, PhD MRC Cognition and Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF United Kingdom Phone +44 1223 273632 (direct line) From dgwakeman at gmail.com Tue Nov 9 12:24:45 2010 From: dgwakeman at gmail.com (dgwakeman at gmail.com) Date: Tue, 9 Nov 2010 17:24:45 +0000 (UTC) Subject: [Mne_analysis] Changing EEG electrodes coordinates Message-ID: <12343334.7313.1289323486017.JavaMail.seven@ap4.p4.uk.7sys.net> Simply convert the freesurfer patch to ascii (using freesurfer's mris convert) and read it into matlab -- I sent this from my 3 mobile -- -original message- Subject: Re: [Mne_analysis] Changing EEG electrodes coordinates From: "Li Su" Date: 09/11/2010 16:59 Dear MNE users, I would like to convert a 3D STC structure to a 2D matrix in Matlab which represents the flattened brain. It doesn't matter too much if I lose some areas of the brain, e.g. the medial wall, or the 2D map is slightly distorted. Apparently, MNE can visualise this, but it is not clear to me if I can export the 2D map to Matlab. Many thanks for your help, Li Su -- Li Su, PhD MRC Cognition and Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF United Kingdom Phone +44 1223 273632 (direct line) _______________________________________________ Mne_analysis mailing list Mne_analysis at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From ghumana at mail.nih.gov Tue Nov 9 16:15:00 2010 From: ghumana at mail.nih.gov (Ghuman, Avniel (NIH/NIMH) [F]) Date: Tue, 9 Nov 2010 16:15:00 -0500 Subject: [Mne_analysis] MEG SNR In-Reply-To: Message-ID: Hi Everyone, Does anyone know of a good reference regarding the approximate SNR of unaveraged neural activity measured by MEG? I just need a ballpark estimate. Many thanks in advance. Avniel Ghuman, Ph.D. Postdoctoral Research Fellow Laboratory of Brain and Cognition, NIMH 10 Center Drive Room 4C116, MSC 1366 Bethesda, MD 20892-1366 From hari at nmr.mgh.harvard.edu Tue Nov 9 17:30:28 2010 From: hari at nmr.mgh.harvard.edu (Hari Bharadwaj) Date: Tue, 9 Nov 2010 17:30:28 -0500 (EST) Subject: [Mne_analysis] MEG SNR In-Reply-To: References: Message-ID: <48288.172.21.16.50.1289341828.squirrel@mail.nmr.mgh.harvard.edu> Hi Avniel, Comparing the spectra of raw MEG with the spectra obtained from MEG recorded with no subject (empty room data) if you have access to it might not be a bad way to set the SNR values. We use 3 for the SNR of unaveraged data. This seems to agree roughly with the size of the spectra of resting state MEG and empty room MEG (atleast upto 55 Hz). We have a triple shielded room though. Regards, Hari On Tue, November 9, 2010 4:15 pm, Ghuman, Avniel (NIH/NIMH) [F] wrote: > Hi Everyone, > > Does anyone know of a good reference regarding the approximate SNR of > unaveraged neural activity measured by MEG? I just need a ballpark > estimate. Many thanks in advance. > > Avniel Ghuman, Ph.D. > Postdoctoral Research Fellow > Laboratory of Brain and Cognition, NIMH > 10 Center Drive > Room 4C116, MSC 1366 > Bethesda, MD 20892-1366 > > _______________________________________________ > Mne_analysis mailing list > Mne_analysis at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis > > > -- Hari Bharadwaj From ghumana at mail.nih.gov Tue Nov 9 17:47:04 2010 From: ghumana at mail.nih.gov (Ghuman, Avniel (NIH/NIMH) [F]) Date: Tue, 9 Nov 2010 17:47:04 -0500 Subject: [Mne_analysis] MEG SNR In-Reply-To: <48288.172.21.16.50.1289341828.squirrel@mail.nmr.mgh.harvard.edu> Message-ID: Hi Hari, Thanks, I actually could use a reference to respond to a pesky reviewer if you know of one... Best Wishes, Avniel On 11/9/10 5:30 PM, "Hari Bharadwaj" wrote: Hi Avniel, Comparing the spectra of raw MEG with the spectra obtained from MEG recorded with no subject (empty room data) if you have access to it might not be a bad way to set the SNR values. We use 3 for the SNR of unaveraged data. This seems to agree roughly with the size of the spectra of resting state MEG and empty room MEG (atleast upto 55 Hz). We have a triple shielded room though. Regards, Hari On Tue, November 9, 2010 4:15 pm, Ghuman, Avniel (NIH/NIMH) [F] wrote: > Hi Everyone, > > Does anyone know of a good reference regarding the approximate SNR of > unaveraged neural activity measured by MEG? I just need a ballpark > estimate. Many thanks in advance. > > Avniel Ghuman, Ph.D. > Postdoctoral Research Fellow > Laboratory of Brain and Cognition, NIMH > 10 Center Drive > Room 4C116, MSC 1366 > Bethesda, MD 20892-1366 > > _______________________________________________ > Mne_analysis mailing list > Mne_analysis at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis > > > -- Hari Bharadwaj The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From alexander.hunold at tu-ilmenau.de Wed Nov 10 21:08:28 2010 From: alexander.hunold at tu-ilmenau.de (Alexander Hunold) Date: Wed, 10 Nov 2010 19:08:28 -0700 Subject: [Mne_analysis] shift in freeview Message-ID: <009e01cb8145$56867510$03935f30$@hunold@tu-ilmenau.de> Dear experts, I am perplexed how to fix the problem which is shown in the pictures. The volume is the T1.mgz. The surfaces are computed by MNE (red - inner_skull, yellow - outer_skull, green - outer_skin). In TkMedit the inner and outer skull are aligned to the T1.mgz, respectively. I used and to get the surfaces. I get the same shift with all surfaces I compute with mne_write_surface, as well. Since I would like to visualize 3-4 surfaces with a mri volume I would like to use freeview instead of TkMedit. Do you have any hint how to fix that shift problem? Thanks so much, Alexander -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101110/12583aaf/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: T1_bem_sagittal_freeview.jpeg Type: image/jpeg Size: 209238 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101110/12583aaf/attachment.jpeg -------------- next part -------------- A non-text attachment was scrubbed... Name: T1_bem_tkmedit.jpeg Type: image/jpeg Size: 31672 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101110/12583aaf/attachment-0001.jpeg From dgwakeman at gmail.com Wed Nov 10 21:23:52 2010 From: dgwakeman at gmail.com (Daniel G Wakeman) Date: Thu, 11 Nov 2010 02:23:52 +0000 Subject: [Mne_analysis] shift in freeview In-Reply-To: <009e01cb8145$56867510$03935f30$@hunold@tu-ilmenau.de> References: <009e01cb8145$56867510$03935f30$@hunold@tu-ilmenau.de> Message-ID: <724DF96D-57F5-42A1-9BCF-54A86ABC70E6@gmail.com> Dear Alexander, This question is probably better off answered on the freesurfer list than the MNE list, since it is a freesurfer question (mne_watershed_bem simply uses freesurfer to generate the surfaces (as described in the manual)). My suspicion is that freeview (which I believe is still in beta), is utilizing the nifti origin, while by default freesurfer calculates surfaces with it's own origin (http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems). If you only care about the visualization, the easy thing to do would be to first find out what coordinate frame it does use second read in the surfaces in matlab (for example) and perform the translation (plus any rotations if necessary, though it doesn't appear as though that is). Save these new surfaces under different names (so as not to cause problems with your MNE calculations). e.g. inner_skull.freeview Then use these for visualization. D On 2010 Nov 11, at 02:08 , Alexander Hunold wrote: > Dear experts, > > > > I am perplexed how to fix the problem which is shown in the pictures. > The volume is the T1.mgz. The surfaces are computed by MNE (red - > inner_skull, yellow - outer_skull, green - outer_skin). In TkMedit the inner > and outer skull are aligned to the T1.mgz, respectively. > > I used and to get the > surfaces. > > I get the same shift with all surfaces I compute with mne_write_surface, as > well. > > Since I would like to visualize 3-4 surfaces with a mri volume I would like > to use freeview instead of TkMedit. > > Do you have any hint how to fix that shift problem? > > > > Thanks so much, > Alexander > > _______________________________________________ > Mne_analysis mailing list > Mne_analysis at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From alexander.hunold at tu-ilmenau.de Thu Nov 11 12:41:04 2010 From: alexander.hunold at tu-ilmenau.de (Alexander Hunold) Date: Thu, 11 Nov 2010 10:41:04 -0700 Subject: [Mne_analysis] deal with symbolic link Message-ID: <002601cb81c7$9ed38b50$dc7aa1f0$@hunold@tu-ilmenau.de> Dear experts, I have mri images for one subject and followed the guideline in A.2.1 (MNE manual) to organize the dicoms. So far I am fine. After that I followed the description in A.2.2 and created the symbolic links to and . The script mne_flash_bem cancels with following error in the error.log (in ): file not found or unknown file type for file flash/009/09360159 My current directory in the terminal is the directory. I appreciate any hint. Thanks so much in advance. Sincerely, Alexander PS: For short term (6 weeks), I am working under Kubuntu. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101111/72422ec8/attachment.html From csp6107989 at 126.com Tue Nov 30 02:33:01 2010 From: csp6107989 at 126.com (=?GBK?B?sszJ3MZN?=) Date: Tue, 30 Nov 2010 15:33:01 +0800 (CST) Subject: [Mne_analysis] mne_raw2mat Message-ID: <686563c4.2022b.12c9bb2e4dd.Coremail.csp6107989@126.com> I want to convert fif file to mat file, when I run mne_raw2mat,it say "(" unexpected (expecting "fi"). Pleseas tell me how can I resolve this problem. First,I am a Chinese student Second,I am a greenhand Linux user.My Linux system is ubuntu 9.04. More details is better.Thanks for your help? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101130/7f06d6bb/attachment.html From Elena.Orekhova at neuro.gu.se Fri Nov 12 17:29:21 2010 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 12 Nov 2010 22:29:21 -0000 Subject: [Mne_analysis] averaging of different event types Message-ID: <32CC77C0C8A7AD4B9410934642608E1F01C732@exchccr1.neuro.gu.se> Hi, I have to average events that have different values (e.g. 1 and 65 or 4097 and 4161) on the ?STI 014? trigger channel. What is the easiest way to do it? Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20101112/4c098735/attachment.html