- ynic-users

FW: Freesurfer @ YNiC - IMPORTANT UPDATE
by Tom Hartley 30 Nov '07

30 Nov '07

Dear list, I do hope this (general availability of Freesurfer) will happen soon, as the tool looks very useful indeed, and Pádraig's results shows it achieves good results without manual intervention. You can use for a variety of important analyses that are simply not possible in e.g., FSL, SPM *Reconstruct the cortical surface and project functional data onto it - very important in understanding topographical organization of cortical function (e.g., retinotopy) which is otherwise obscured in the volumetric data. *Automatically identify/label cortical regions on the basis of anatomical landmarks (e.g., fusiform gyrus, motor cortex etc.) Good for anatomical ROIs *Automatically identify/label "subcortical" regions (i.e., regions not on the cortical surface including amygdala, hippocampus, caudate etc.) Good for anatomical ROIs and volumetry *Analyse functional group data in a more meaningful space (i.e., one in which different subjects cortical surfaces are aligned to shared sulcal landmarks) Good for statistical significance? *Measure local cortical thickness, curvature etc. Useful for structural analysis. I have placed some pictures onto my web page to give an idea of the segmentation possibilities http://www-users.york.ac.uk/~th512/cortical_seg_neuroimage.jpg http://www-users.york.ac.uk/~th512/subcortical_seg_neuron.jpg Check out their publications for more information: http://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndPosters Many thanks to Pádraig for his sterling work in blazing this trail. Best wishes, Tom Hartley (BTW I tried mailing the pictures as attachments, and but the message got stuck on the server - the mailing list doesn't forward messages over 40KB) -----Original Message----- From: Pádraig Kitterick [mailto:p.kitterick@psych.york.ac.uk] Sent: 29 November 2007 17:34 To: ynic-users(a)ynic.york.ac.uk Subject: Re: Freesurfer @ YNiC - IMPORTANT UPDATE Dear list, Please ignore my previous instructions for installing freesurfer on YNIC machines. Gary and Mark have just pointed out a very critical point about doing this: due to the size of the freesurfer package (>3Gb), it is not feasable to have users installing their own copies of the software as the disk usage would be considerable. YNIC are looking into ways of provide freesurfer to all users from a central location sometime in the future. Apologies for any confusion, Padraig Pádraig Kitterick wrote: > Dear list, > > If anyone else is considering using Freesurfer > (http://surfer.nmr.mgh.harvard.edu/) to reconstruct cortical surface > models from T1 volumes collected at YNiC, you might be interested in > the following information. > > By default, if you feed a standard structural YNIC T1 into freesurfer > it will most likely produce spurious brain extractions, and have great > difficulty (read: 40+ hours of processing!) in reconstructing the > cortical surfaces. After exploring these problems for a while, I > discovered two issues which require some pre-processing to solve. The > first is that freesurfer does not like images with a FOV larger than > 256mm^3. Standard YNIC T1 structurals have a FOV measuring > 176x290x290mm > (176x256x256 slices of 1 x 1.13 x 1.13mm). > > In addition to this, the voxel dimensions are misinterpreted by > freesurfer when it attempts to resample the volume to 1x1x1m voxels, > which it does as a standard part of the importing process. They are > interpreted incorrectly as 1.13 x 1.13 x 1mm! Needless to say, this > leads to all kinds of problems, resulting in spatially distored output > surfaces. > > Therefore, I would recommend that the following steps are taken before > trying to carry out any processing with freesurfer: > > 1) Manually resample the T1 to 1x1x1mm and force the correct > dimensions to be used, with the 'mri_convert' command (part of the freesurfer package): > > mri_convert -iis 0.9999 -ijs 1.1328 -iks 1.1328 -ois 1 -ojs 1 -oks 1 > -oic 176 -ojc 290 -okc 290 T1.nii.gz T1_1mm.nii.gz > > Here, we specify the input sizes (1x1.13x1.13mm), the output sizes > (1x1x1mm), and I have also specified the number of output slices which > is important because otherwise mri_convert will truncate them to a > maximum of 256. > > N.B.: This command _should_ be identical for all standard YNIC T1 > structurals. However, it is always important to check that your slice > counts and sizes are the same as the example given here, otherwise all > subsequent processing will be compromised. > > 2) Remove unnecessary slices from outside the head and the neck so > that the final number of slices is less than or equal to 256 in all > dimensions with avwroi (from fsl): > > avwroi T1_1mm T1_1mm_reslice x_start x_size y_start y_size z_start > z_size > > where T1_1mm is the resampled MRI (no .nii.gz extension), > T1_1mm_reslice is the output volume (again, no .nii.gz extension), and > the _start and _end parameters specify the starting slice and the > number of slices to include in each dimension (use fslview to find the > slice numbers). For example, to remove the first and last 17 slices in > the Y and Z dimensions, we could run: > > avwroi T1_1mm T1_1mm_reslice 1 176 18 256 18 256 > > which would leave us with a FOV of 176x256x256mm, compatible with > freesurfer. Be careful that only redundant slices are removed! > > Your pre-processed volume should now consist of less than or equal to > 256 slices in each dimension, with 1x1x1mm voxels. This can be safely > processed with freesurfer using: > > recon-all -i T1_1mm_reslice.nii.gz -subjid <subject id> -autorecon-all > > Finally, make sure you apply all of this to a copy of the T1, as you > won't be able to modify the original in the mridata folder, and even > if you can you really shouldn't! > > I hope this will save someone a bit of time and a lot of headaches! > > p.s. if you want to install freesurfer in your home folder on YNIC > machines, follow these steps: > 1) Download the freesurfer PowerPC distribution and register for a > licence file on their website: http://surfer.nmr.mgh.harvard.edu/ > 2) Double-click on the image file, and a window will open which > contains a single package file. > 3) Right-click on the package file and choose 'Show pacakge contents' > 4) In the new window that opens, navigate into the 'Contents' folder, > and drag the Archive.pax.gz to your desktop. > 5) Double click on the archive file and wait for it to decompress > (this will take a long time)... > 6) You should now have a freesurfer folder on your desktop, which you > can drag into your home folder. Now remove the archive files on your > desktop as they are quite large and are no longer needed. > 7) Open a text editor and copy&paste the following: > > export FREESURFER_HOME=~/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > and save the file as 'freesurfer-config' in your home folder. Note > that this script presumes that you have moved the freesurfer folder > into your home folder. > 8) Copy your licence file into your freesurfer folder. > 9) In an X terminal, type 'source ~/freesurfer-config'. You can now > use freesurfer commands. Make sure you run this command in X11 each > time you log in to have access to freesurfer. > > Padraig. > -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk -- ynic-users mailing list ynic-users(a)ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users

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Freesurfer @ YNiC
by Pádraig Kitterick 29 Nov '07

29 Nov '07

Dear list, If anyone else is considering using Freesurfer (http://surfer.nmr.mgh.harvard.edu/) to reconstruct cortical surface models from T1 volumes collected at YNiC, you might be interested in the following information. By default, if you feed a standard structural YNIC T1 into freesurfer it will most likely produce spurious brain extractions, and have great difficulty (read: 40+ hours of processing!) in reconstructing the cortical surfaces. After exploring these problems for a while, I discovered two issues which require some pre-processing to solve. The first is that freesurfer does not like images with a FOV larger than 256mm^3. Standard YNIC T1 structurals have a FOV measuring 176x290x290mm (176x256x256 slices of 1 x 1.13 x 1.13mm). In addition to this, the voxel dimensions are misinterpreted by freesurfer when it attempts to resample the volume to 1x1x1m voxels, which it does as a standard part of the importing process. They are interpreted incorrectly as 1.13 x 1.13 x 1mm! Needless to say, this leads to all kinds of problems, resulting in spatially distored output surfaces. Therefore, I would recommend that the following steps are taken before trying to carry out any processing with freesurfer: 1) Manually resample the T1 to 1x1x1mm and force the correct dimensions to be used, with the 'mri_convert' command (part of the freesurfer package): mri_convert -iis 0.9999 -ijs 1.1328 -iks 1.1328 -ois 1 -ojs 1 -oks 1 -oic 176 -ojc 290 -okc 290 T1.nii.gz T1_1mm.nii.gz Here, we specify the input sizes (1x1.13x1.13mm), the output sizes (1x1x1mm), and I have also specified the number of output slices which is important because otherwise mri_convert will truncate them to a maximum of 256. N.B.: This command _should_ be identical for all standard YNIC T1 structurals. However, it is always important to check that your slice counts and sizes are the same as the example given here, otherwise all subsequent processing will be compromised. 2) Remove unnecessary slices from outside the head and the neck so that the final number of slices is less than or equal to 256 in all dimensions with avwroi (from fsl): avwroi T1_1mm T1_1mm_reslice x_start x_size y_start y_size z_start z_size where T1_1mm is the resampled MRI (no .nii.gz extension), T1_1mm_reslice is the output volume (again, no .nii.gz extension), and the _start and _end parameters specify the starting slice and the number of slices to include in each dimension (use fslview to find the slice numbers). For example, to remove the first and last 17 slices in the Y and Z dimensions, we could run: avwroi T1_1mm T1_1mm_reslice 1 176 18 256 18 256 which would leave us with a FOV of 176x256x256mm, compatible with freesurfer. Be careful that only redundant slices are removed! Your pre-processed volume should now consist of less than or equal to 256 slices in each dimension, with 1x1x1mm voxels. This can be safely processed with freesurfer using: recon-all -i T1_1mm_reslice.nii.gz -subjid <subject id> -autorecon-all Finally, make sure you apply all of this to a copy of the T1, as you won't be able to modify the original in the mridata folder, and even if you can you really shouldn't! I hope this will save someone a bit of time and a lot of headaches! p.s. if you want to install freesurfer in your home folder on YNIC machines, follow these steps: 1) Download the freesurfer PowerPC distribution and register for a licence file on their website: http://surfer.nmr.mgh.harvard.edu/ 2) Double-click on the image file, and a window will open which contains a single package file. 3) Right-click on the package file and choose 'Show pacakge contents' 4) In the new window that opens, navigate into the 'Contents' folder, and drag the Archive.pax.gz to your desktop. 5) Double click on the archive file and wait for it to decompress (this will take a long time)... 6) You should now have a freesurfer folder on your desktop, which you can drag into your home folder. Now remove the archive files on your desktop as they are quite large and are no longer needed. 7) Open a text editor and copy&paste the following: export FREESURFER_HOME=~/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh and save the file as 'freesurfer-config' in your home folder. Note that this script presumes that you have moved the freesurfer folder into your home folder. 8) Copy your licence file into your freesurfer folder. 9) In an X terminal, type 'source ~/freesurfer-config'. You can now use freesurfer commands. Make sure you run this command in X11 each time you log in to have access to freesurfer. Padraig. -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk

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booking MRI slots
by Gary Green 29 Nov '07

29 Nov '07

Dear users We are, fortunately, being increasing asked to provide clinical scanning slots for the NHS and for Lodestone. This has the desirable effect of providing income. It has the disadvantage that there is less flexibility in being able to offer slots for research scanning, especially when the research is part of a pilot project that is unfunded. The agreement with Lodestone is that they will attempt to use free slots left after the Thursday noon cut-off for booking by research PIs. Please book your time for the week ahead by booking before Thursdays at noon. Lodestone will then take the remaining slots for single case work. The only exception to this is Lodestone NHS work which will continue to occupy half day slots so that block booking of patients can be used several weeks ahead of time. There is little pressure on scanners in the evenings (at the moment). If you are a trained operator then please consider using evening slots for your research. If you wish to become trained in operating MRI then please let us know so that we can start a training course for those interested. The advantage is that evening scanning is cheaper, at the moment. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Important news update
by Gary Green 28 Nov '07

28 Nov '07

Dear ynic-users At the Thursday evening sessions this term we have been describing the changes in YNiC and building up to the first official release of YNiC software and documentation. We are very pleased to be able to announce that the release date will be the 8th of January 2008. This is earlier than we had originally planned and reflects the enormous amount of effort that everyone has put into getting the software and documents into a complete package. This could not have been done without the co-operation of the users who carried out the beta testing. Further information about the complete contents of the first release will be circulated next week. We had initially planned to hold masterclasses this term to go through current software and applications. But as we can now confidently say that the new software will be released early in the new year, it makes sense to hold the masterclasses after that release so that everyone can take full advantage of all the new features and the more complete help documentation. Therefore we would like to postpone the masterclasses. Instead we would like to hold the roundtable discussion on the use of the eye-tracker. We also have a new user who would like to make a project presentation. We would like to suggest that the Thursday sessions now look like this for the rest of term Thursday 29th Nov 2007 : Project presentation by Dr. Srimant Tripathy from Bradford Thursday 6th December : Roundtable discussion on use of the eye-trackers Thursday 13th December : Project presentation by Gary Green Thursday 20th December : Christmas drinks and then Thursday 10th January 2008 : The new software and documentation Thursday 17th Jan : Masterclass on the new visualisation software Thursday 24th Jan : Masterclass on MEG analysis techniques Thursday 31st Jan : Masterclass on MRI analysis techniques We then propose that we start the roundtable discussions about what should be in the second release comments welcome -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Thursday seminar
by Will Woods 21 Nov '07

21 Nov '07

November 22nd 1. Update on analysis tools at YNiC 2. MRI FSL 2.1 Features: Atlases, Bedpostx and FIRST, avw2fsl 2.2 Scripts and batch processing (python demo) 2.2 Higher level analyses (?) 2.3 Cluster Feat and Cluster Other OTHER (Freesurfer, SPM, mrVista) 3. MEG tools 3.1. Beamforming and permutation statistics 4. Visualisation tools at YNiC 4.1 FSLVIEW 4.2 YNICDV3D 5. Support & Documentation at YNiC 6. Users' requests and what we can do better All welcome, refreshments will be provided afterwards. -- Will Woods York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk

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Bas Science link
by Michael Simpson 19 Nov '07

19 Nov '07

Dear all, Brain Imaging has reached the pages of Ben Goldacre's Guardian column, Bad Science. http://www.badscience.net/2007/11/this-is-your-brain-this-is-your-brain-on-… Thought some of you may be interested, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Re: Event-Related optimum schedule
by Tim Andrews 15 Nov '07

15 Nov '07

Hi Laura, Rapid event-related fMRI has many advantages for cognitive neuroscience research. However, the main problem with this technique is that the signal is very small compared to a block design. One way to increase the signal-to-noise ratio is to increase the number of trials. This typically means using a short ISI (otherwise your subjects could be in the scanner for a long time!). It is also good to vary the ISI to avoid expectation effects (i.e the subject predicting when the next event is likely to occur). However, the problem with a short ISI is that the response to one stimulus will likely overlap with the response to the next. This is not a problem if the BOLD response is linear (i.e. the response to two successive stimuli is the same as adding the response to two independent stimuli with an appropriate temporal offset). However, a number of studies have found that there are significant non-linearities when the ISI is less than ~5sec (eg Dale and Buckner, 1997; Huetell and McCarthy, 2000). So, varying ISI can have positive and negative effects on the BOLD signal. I haven't used the programs that Claire and Silvia are using, but I assume they are trying to find an optimum balance between these effects. Users - please feel free to correct or comment! Tim Laura Lee wrote: > Hi MRI-support, > > I'm struggling along trying to work out how to create a 'stochastic' > event-related design for fMRI. Claire Moody has passed on a program > that searches for the optimum stimulus schedule (she & Silvia used it > for their last project). I've read over all the bumpf but am still > quite confused by all the new concepts. I think I know roughly what I > want but then there are some parameters I am unsure about and don't > really understand the implications of the settings. I'd be really > grateful if you could give me a hand. > > This is the programme I downloaded... > http://surfer.nmr.mgh.harvard.edu/optseq > And there's a pretty comprehensive help page here... > http://surfer.nmr.mgh.harvard.edu/optseq/optseq2.help.txt > > Thanks, Laura > > > > > -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

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Interesting (short) paper
by Michael Simpson 15 Nov '07

15 Nov '07

Dear all, there is another interesting paper in the 'Articles of interest' section of: https://www.ynic.york.ac.uk/doc/Miscellaneous This one is on combined MRI / MEG, which may or may not be of interest you. If you have any papers to add to this section, forward them to me and I'll make them globally available. Thanks, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Seminars today
by Gary Green 15 Nov '07

15 Nov '07

Elena Solesio has been visiting YNiC from the imaging centre in Madrid. Today, Thursday lunchtime, at 1:00pm, Elena will be giving a talk in YNiC open plan on some of the work she's been doing, entitled: Retroactive Interference Modulates Magnetic Brain Activity In Normal Aging: A Magnetoencephalography Study. All are welcome to come along. ----------- At 4pm today, there is a YNiC update seminar 1. update on MEG 2. recap of MEG facilities at YNiC 3. what is new and what has changed 4. sensor space and source space 5. beamforming update 6. minimum norm and dipoles 7. Users' requests and what we can do better All welcome Refreshments will be served after the seminar -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Thursday lunchtime seminar
by Sam Johnson 12 Nov '07

12 Nov '07

Hello all, Elena Solesio has been visiting YNiC from the imaging centre in Madrid. This Thursday lunchtime, at 1:00pm, Elena will be giving a talk in YNiC open plan on some of the work she's been doing, entitled: Retroactive Interference Modulates Magnetic Brain Activity In Normal Aging: A Magnetoencephalography Study. As ever all are welcome to come along. Thanks, Sam

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Connectivity seminar this spring?
by Johan Carlin 12 Nov '07

12 Nov '07

Dear All, I would really like to see a Thursday session on connectivity - dynamic causal modelling, diffusion tensor imaging, etc. Is this interesting to anyone else? Best, Johan Carlin

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[Fwd: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 11, 2007]
by Tim Andrews 12 Nov '07

12 Nov '07

Paper on Bloodless MRI that might be of interest to some of you in the latest TINS -------- Original Message -------- Subject: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 11, 2007 Date: Sat, 10 Nov 2007 13:43:30 -0500 From: ScienceDirect Message Center <valert(a)prod.sciencedirect.com> To: ta505(a)york.ac.uk ScienceDirect <http://www.sciencedirect.com/science> New Volume/Issue is now available on ScienceDirect Trends in Neurosciences <http://www.sciencedirect.com/science/issue/4872-2007-999699988-673508> Trends in Neurosciences <http://www.sciencedirect.com/science/journal/01662236> Volume 30, Issue 11 <http://www.sciencedirect.com/science/issue/4872-2007-999699988-673508>, Pages 555-610 (November 2007) 1. Editorial Board <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Page i Review 2. From genes to pain: Nav1.7 and human pain disorders <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 555-563 Sulayman D. Dib-Hajj, Theodore R. Cummins, Joel A. Black and Stephen G. Waxman 3. Munc18-1 in secretion: lonely Munc joins SNARE team and takes control <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 564-572 Ruud F.G. Toonen and Matthijs Verhage 4. The TASK background K2P channels: chemo- and nutrient sensors <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 573-580 Fabrice Duprat, Inger Lauritzen, Amanda Patel and Eric Honoré 5. Phosphatase PTEN in neuronal injury and brain disorders <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 581-586 Ning Chang, Youssef H. El-Hayek, Everlyne Gomez and Qi Wan 6. The ubiquitin–proteasome pathway in health and disease of the nervous system <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 587-595 Ashok N. Hegde and Sudarshan C. Upadhya 7. Neuronal ‘On’ and ‘Off’ signals control microglia <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 596-602 Knut Biber, Harald Neumann, Kazuhide Inoue and Hendrikus W.G.M. Boddeke 8. Bloodless fMRI <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 603-610 Alan Jasanoff Send my e-mail in plain text format <http://www.sciencedirect.com/science/account> Modify or Remove My Alerts <http://www.sciencedirect.com/science/alerts> Access the ScienceDirect Info site <http://www.info.sciencedirect.com> if you have questions about this message or other features of this service. This email has been sent to you by ScienceDirect, a division of Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Tel.+31 20 485 3911. ScienceDirect respects your privacy and does not disclose, rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in the ScienceDirect online privacy policy <http://www.sciencedirect.com/science/privacy>. By using email or alert services, you agree to comply with the ScienceDirect Terms and Conditions <http://www.sciencedirect.com/science/termsandcond>. To unsubscribe to alert services, please go to the Alerts <http://www.sciencedirect.com/science/alerts> page. Copyright © 2007 ScienceDirect. All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. ScienceDirect® is a registered trademark of Elsevier B.V. Delivery Job ID: 1929:126069537:1927:108342272 -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

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registration with MRI
by Tim Andrews 01 Nov '07

01 Nov '07

Dear All, Recently, we have had some problems with registration using FSL. Some of the registrations, particularly with the standard brain appear to be quite poor. Jodie, Claire and Andre have done some work on this recently and found that the best combination of registrations in FSL is Initial Structural: 15 degree search, 6 DOF Main Structural: 15 degree search, 6 DOF Standard Brain: 15 degree search, 12 DOF If you have any views on this, could you let us know. We have also noticed that the brain extraction tool, which is set as default on FEAT has not always been removing the skull from the EPI images. If you have been doing FEAT analysis, I would be grateful if you could let us know whether BET has been working for you. If this hasn't been happening, it could affect your registrations. A related issue, is that although structural brain images are automatically skull stripped using BET, FLAIR images are not. However, I believe that BET may be automatically applied to FLAIR images in the near future. :-) Cheers, Tim -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

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seminar today
by Gary Green 01 Nov '07

01 Nov '07

"Off-line consolidation during sleep and wakefulness" Dr Penny Lewis Psychology Department, University of Liverpool Date: 16:00. Thursday 01 November 2007 Location: YNiC Open Plan Host: Gary Green Programme: York Neuroimaging Centre Seminars All welcome Refreshments will be served after the seminar Penny Lewis will be in YNiC this afternoon if individuals would like to meet her. We will be taking Penny out to dinner after the seminar. If you would like to join us for dinner please contact Gary Green. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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brainstorming session and beamforming
by Gary Green 25 Oct '07

25 Oct '07

Dear Users Yesterday we had an extremely useful brainstorming session. The discussion brought to light some issues about using beamforming which have not been reported in the literature yet. As these observations might affect other users we thought it would be of interest to bring them to the attention of all users. Uzma Urooj, supervised by Andy Ellis with Michael Simpson as SLO, had identified two particular puzzling issues when using the beamforming approach to (a) localise time locked activity and (b) create virtual electrodes. (a) the first observation is that if one constructs a NAI map from a beamformer, the statistically significant blobs do not necessarily align with the largest amplitude averaged response seen with virtual electrodes. What the user has done was to perform a standard beamforming analysis of some data and localised the most significant blob. They then placed virtual electrodes at this point and around it. At each of these virtual electrode positions they calculated the average response across epochs. The largest amplitude evoked response was not at the location of the beamformer blob. This observation has also been replicated in simulation studies by Mark Hymers where he has placed dipoles at known locations in a model brain which had realistic background noise. The reason this occurs is because of the way the beamformer works. The beamformer is a set of spatial filters which are designed to measure the brain activity (the NAI) from each brain location in turn. The filters are constructed to ensure that activity only comes from one location at a time. All other locations are suppressed. This is done by computing the power within the MEG signal and ensuring that this is measured with a gain of one from a specified location and that it is zero from all other positions. This is the key point - the beamformer is specified in terms of MEG power. The power in an MEG signal can come from two forms of oscillation, those that are time locked to the stimulus and those power changes that produced by a stimulus but are not time locked in terms of the oscillatory phase (often called the stimulus induced power). Thus the blobs created by the application of the beamformer programme are in terms of total power (time locked and induced). When the average virtual electrodes were computed, these measures were only of time locked activity. The user that brought this to our attention has made an important observation, within a specific region, brain responses that are time locked maybe at a different location to induced power changes. As we do not know the relationship between fMRI haemodynamic changes and MEG oscillations (time locked vs induced), it may be that beamformer results will not always align with fMRI results either. This does not mean that the beamformer is wrong in some way. In means that we have to be very careful in how we interpret beamformer output in terms of blobs and virtual electrodes. There clearly is a need to be able to distinguish between time locked and induced responses. To this end, Will Woods has been working on a 'evoked' beamformer. implications for users of the beamformer NAI statistical maps reflect total power changes within a band and can contain both induced and time locked responses, just induced power changes or just time locked responses. In the latter case the virtual electrode averages will align with the NAI maps. In the other two cases, NAI maps may not align with VE maps. The issue for users is what form of response should be used to test a specific hypothesis. This will be down to the individual user who will have a specified model for their particular experiment in terms of how stimuli may be encoded. NAI maps are estimates of statistical changes in total power, these maps are related to the mean and variance of the power in the oscillations produced by both induced and time locked responses Averages of VEs provide estimates of the average time locked response, only. (b) the second interesting observation made by Uzma related to the construction of time series of virtual electrode activity for every epoch. Uzma has used a specific time window (say 200 milliseconds) to estimate weights for a beamformer. Uzma then used these weights to estimate the virtual electrode time series for a much longer time window beyond that of the original 200 milliseconds for every epoch. The virtual electrode output (three orthogonal components) was manipulated to create an estimate of power as a function of time. This was done by taking the squares of each VE component and summing them. This gives a measure of the power as a function of time for each epoch. Uzma then averaged these power time series, producing the average power changes as a function of time. Uzma made an observation that has not been reported before. Beyond the end of the original 200milliseconds, a large slow change in power was observed. If this was all repeated for a window that was 1000 milliseconds long, the slow change in power was now observed if the power was estimated for times greater than 1 second. This is a very important observation. The current thoughts about this are that this is a property of the beamformer. It might arise as follows. The beamformer weights are estimated from the covariance matrix of the original MEG data within the specified window (say 200 milliseconds). Covariance is related to power within a signal, that is why it is stated that a set of beamformer weights is about detecting the power from a specific location and not any other. If a window is only 200 milliseconds long, a very poor estimate will be made of power below 5Hz (1/0.2). Thus this beamformer will not be able to correctly deal with slow changes in power and estimates beyond the original window may be inaccurate. implications for users of the beamformer When using a beamformer to estimate changes in power (especially induced power) with time, observations are only reliable when made within the time contraints of the original window length that was used to construct the beamformer. The problem with this is that a beamformer works best if the window length matches the duration of the induced power change, especially if performing a statistical comparison between two conditions. If long windows are used and the induced power changes are fractional proportions of the length of the window, then statistical power will be lost. In this case it would be best to use moving windows as in the Pammer and Cornelissen paper. ---------------- I believe this demonstrates that brainstorming sessions are quite important activities. Some people might be concerned about bringing problems to the attention of other users, but as the above demonstrates, it can be invaluable as it can highlight problems that are not fully appreciated. Many thanks to the user who brought this to our attention. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Re : YNiC Seminar this week]
by Gary Green 22 Oct '07

22 Oct '07

October 25th 4pm YNiC Open Plan 1. Project presentation: Michael Simpson 2. Project presentation: Laura Lee 3. Work in progress - a look at an ongoing project All welcome. Refreshments will be available. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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potentially interesting talk
by Silvia Gennari 19 Oct '07

19 Oct '07

I thought I would circulate the following talk to YNiC users as it could be potentially interesting to many users. This is talk presenting results of an fmri experiment after extensive training with different kinds of sounds. Speech-like processing of nonspeech sounds following extensive categorization training. Dr James Keidel, University of Manchester Monday, Oct 22nd, 2007, 12.30pm, C108, Dept of Psychology Silvia Silvia Gennari Department of Psychology University of York Heslington, York YO10 5DD United Kingdom

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Fixation-contingent presentation of stimuli in MEG
by a.ellis＠psych.york.ac.uk 19 Oct '07

19 Oct '07

FIXATION-CONTINGENT PRESENTATION OF STIMULI IN MEG Laura Barca and I ran an MEG experiment in which participants were instructed to fixate on a central point on a screen positioned 1 metre in front of them. A stimulus (e.g. a word) was then presented very briefly to the left or right of the fixation point. The aim was to track the processing through the brain of words presented in the right visual field, projecting directly to the left (language) hemisphere, or in the left visual field, projecting first to the left (non-language) hemisphere and presumably needing to be transferred across to the left hemisphere via the corpus callosum for processing. In the absence of eye movement monitoring we had to trust our participants to fixate centrally, and to rely on the brief presentations to assert that they could not have re-fixated in the time that the stimulus was on the screen. We can also point to differences in the patterns of brain activation we observed as indicating that we were successful on most trials of the experiment in controlling presentation as we wanted to. There are, however, people out there who could end up reviewing grant applications for further work who get very animated about the need for accurate fixation control in this kind of experiment. There are also two strands of future research that may need more accurate monitoring. One is work I would like to do following up Lisa Henderson's MSc project comparing the responses of dyslexic and non-dyslexic students to words presented in the left and right visual fields. The other is a project by a PhD student of Richard Wise at Imperial College London , Zoe Woodhead (a former undergraduate of ours), who want to use the York MEG system to look at word recognition in patients with hemianopias following occipital strokes. Both dyslexic and hemianopic participants may be assumed to have greater difficulty controlling their fixation than 'normal' participants, and good fixation control would be especially helpful for those studies. It would also help with studies I would like to do in which words will be presented centrally on the assumption that certain letters fall to the left of fixation while other letters fall to the right. What would be nice to have, then, is a way of ensuring that stimuli are only displayed on the screen when a participant is fixating on, or close to, a central fixation point. We normally offset the inner edge of our stimuli by 1.5 degrees, so it would be good to define a central fixation sphere with a radius of 0.5 degrees at 1 m distant from the participant, and only to present the stimulus on a given trial when fixation is within that sphere. So: 1. Would the resolution of the system allow us to know when someone is fixating within a sphere that has a diameter of 1 degree at 1 metre distance? Is a smaller resolution possible? 2. What would be the minimum time between registering that fixation is within the defined region and a stimulus appearing on the screen? I want to avoid suggestions that participants may have moved their eyes in the interval between fixation being registered and the stimulus being presented. It might help to present the stimulus after fixation has been within the central sphere for a certain period of time in order to exclude the possibility that participants were sweeping their eyes through the sphere when presentation was triggered. 3. Richard Wise and Zoe Woodhead would be interested in a variant of this procedure where a stimulus remains on the screen for as long as fixation remains within the central region. This would allow more prolonger presentation of stimuli to, for example, patients with hemianopias whose processing of visual inputs may be relatively slow. I know that Richard and Zoe have toyed with presenting "sentences" in one or other visual field by displaying one word after another at the same position. That would be OK to do if we could know that fixation remained central throughout. 4. Finally, I gather from the meeting last night that only one eye is monitored. There is quite a lot of discussion in the literature about how often the two eyes focus on the same point, and how often there is either 'crossed' or 'uncrossed' fixation. We would need to think about this, and whether we should, for example, put a patch over the unmonitored eye. I am posting this on ynic-users because we were encouraged to do so. I am hoping for a sober response from YNiC which is realistic about what could and could not be done, any difficulties we may run into, and the time that would be required to implement a system like this (assuming that it is do-able). At the moment all I need to know is what could or could not be achieved so that I can write that in confidence into grant applications. Other people with an interest in vision and MEG (Silvia, Piers, Andy Y etc) may want to chip in so that YNiC can get a fuller understanding of what people would like to have in the way of intergrated fixation monitoring and stimulus presentation. Andy Ellis 19 Oct 2007

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YNiC Seminar this week
by Gary Green 17 Oct '07

17 Oct '07

October 18th 4pm YNiC Open Plan 1. This autumn in YNiC - the programme 2. What is new and what has changed 3. Booking and the database 4. Ethics and governance 5. new tools 6. The support system explained 7. What is happening in YNiC - a look at the future 8. A discussion about users' needs and a new forum for getting users involved All welcome. Refreshments will be available. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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MEG and MRI
by Gary Green 17 Oct '07

17 Oct '07

You will probably be pleased to hear that MEG is now fully operational again. We have also taken time to get the system recalibrated, eye trackers installed and a complete overhaul of the mechanics of the bed. The noise level is lower as the source of the small electrical pulse artefacts has been identified and removed. All MEG channels are working. The original problem was due to a faulty interface between the fibre optics taking data out of the shielded room into the data acquisition rack. The board has been replaced. Bookings can now be taken for MEG. You may also be pleased to hear that MRI has had a routine maintenance and all is well. happy scanning! -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Fwd: Visual Dysfunction and Cognition in Childhood
by Andy Ellis 08 Oct '07

08 Oct '07

> > >Please bring this conference to the attention of colleagues who may >be interested- > >BPS Division of Neuropsychology > > >Visual Dysfunction and Cognition in Childhood > >This day conference will increase knowledge on psychological, >neurological and neurobiological systems involved in vision and >visual defects of brain and peripheral optic pathways. it will also >increase knowledge on brain:cognition relationships and cognitive >patterns associated with visual defects, including spatial >cognition, and severe visual impairment. The conference introduces >the latest theory and practice in these areas, including clinical >assessment and interpretation of cognitive development and disorders >in children with severe visual impairment. > >Date: 30 October 2007 > > >Who should attend? > >This event is open to clinical or educational practitioners or >researchers in child neuropsychology, clinical child psychology, >paediatric, neurology, occupational therapists and related >neuroscience disciplines. Relevant to practitioners and researchers. > > >Programme > >09:30 Registration & Refreshments > >10:00 Two visual systems: agnosia, optic ataxia & neglect > >Professor David Milner (Professor of Cognitive Neuroscience, >University of Durham): Co-author of Sight Unseen (winner of the BPS >Book Award) > >11:15 Refreshments > >11:30 Neurobiological models of visual-spatial deficits in childhood > >Professor Janette Atkinson (Director of Visual Development Unit: >University College London/ Oxford University): Author of The >Developing Visual Brain > >12:45 Lunch > >14:00 Visual impairment and cognition: neurodevelopmental issues > >Dr Naomi Dale (Head of Psychology (Neurodisability), Great Ormond >Street Hospital/ UCL Institute of Child Health): Co-lead in >developing the governmental Early Support Developmental Journal for >parents and children with VI > >14:45 Refreshments > >15:00 Visual impairment and cognition: clinical assessment and >interpretation > >Dr Naomi Dale (Head of Psychology (Neurodisability), Great Ormond >Street Hospital/ UCL Institute of Child Health): Co-lead in >developing the governmental Early Support Developmental Journal for >parents and children with VI > >15:45 Concluding Remarks > > >Speakers > >Professor David Milner (University of Durham): Co-author of Sight >Unseen (winner of the BPS Book Award) > >Professor Janette Atkinson (University College London/ Oxford >University): Author of The Developing Visual Brain > >Dr Naomi Dale (Great Ormond Street Hospital/ UCL Institute of Child >Health): Co-lead in developing the governmental Early Support >Developmental Journal for parents and children with VI. >Location Directions >UCL Institute of Child Health, London > >For further details click here- >http://www.ich.ucl.ac.uk/education/short_courses/courses/2S18 > >--------------------------------------------- >COGNEURO archives and subscription manager can be found at >http://www.jiscmail.ac.uk/lists/COGNEURO.HTML >--------------------------------------------- >List owner's email address: COGNEURO-request(a)jiscmail.ac.uk -- Professor Andy Ellis Department of Psychology University of York York YO10 5DD England Tel. +44 (0)1904 433140 http://www.york.ac.uk/depts/psych/www/people/biogs/awe1.html

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Draft programme for Thursdays at YNiC
by Gary Green 21 Sep '07

21 Sep '07

Attached is the 'draft' programme for YNiC Thursday evening seminars for the autumn and early winter. The current plan is that after Christmas the seminars would mainly consist of invited speakers, internal speakers and journal club. The third term would be devoted to people giving talks about work that has been or is about to be published from YNiC projects. ALL comments are welcome. Your ideas are absolutely essential to running a Centre that will make imaging research possible and fun for all. Please send your comments to me, Sam Johnson (science.manager(a)ynic.york.ac.uk) or Tony Morland (a.morland(a)psych.york.ac.uk) Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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[Re : Project presentations : Today
by Gary Green 20 Sep '07

20 Sep '07

Today we have two new project presentations (Thursday the 20th at 4pm in YNiC Open Plan) Project presentations will be made by Professor P. O'Higgins. HYMS. Scalp and head reconstruction from MRI. Dr. T. Jellema, University of Hull, Department of Psychology. Imaging in Autism. We will also announce what is being discussed for YNiC for the autumn term. Do come along and discuss training requirements, seminars and any other issues you would like to see scheduled for a Thursday afternoon. All welcome. refreshments will be available. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Thursday Evening Sessions this autumn
by Gary Green 18 Sep '07

18 Sep '07

We are currently planning the Thursday evening sessions and other training sessions for next term. If you have any thoughts or ideas we would be keen to hear your views. The main sessions will start on the 18th of October. This week though we have two new project presentations (Thursday the 20th at 4pm in YNiC Open Plan) Project presentations will be made by Professor P. O'Higgins. HYMS. Scalp and head reconstruction from MRI. Dr. T. Jellema, University of Hull, Department of Psychology. Imaging in Autism. We will also announce what is being discussed for YNiC for the autumn term. Do come along and discuss training requirements, seminars and any other issues you would like to see scheduled for a Thursday afternoon. We will circulate the draft timetable and ask for comments by email as well. All welcome. refreshments will be available. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Update on MEG
by Gary Green 17 Sep '07

17 Sep '07

I am sorry to say that MEG is still unavailable. 4D are working on the problem and believe that they have determined the cause. We expect an engineer to visit this week and ti make adjustments to the main power supplies to the system. As soon as MEG is available I will let you know. MRI is working fine Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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