ynic-users November 2007

ynic-users@ynic.york.ac.uk

11 participants
15 discussions

MEG talk on Monday (3rd Dec) @ Psychology
by Shane Lindsay 30 Nov '07

30 Nov '07

Dear list, The Psycholinguistics Research Group will be hosting a talk by Eytan Zweig, who has recently joined the linguistics department at York. He will be discussing MEG work carred out with Liina Pylkkänen at NYU investigating a visual M170 effect of morphological complexity. The talk will be held in A202, at 12.30 Monday 3rd, and should last around an hour. Shane

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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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