- ynic-users

MEG Masterclass - Thursday 6th February
by Michael Simpson 06 Feb '08

06 Feb '08

Dear all, this is just a reminder that the MEG masterclass will take place tomorrow. A number of you contacted Andre at the start of the masterclasses to let him know that you are likely to attend these sessions. If you haven't previously let him know of your interest for the MEG class, and would like to attend, please contact *me* so that we can have a rough idea of numbers. The session will take place from 2.30 till 5.00 in Open Plan. 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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Re :MRI corridor
by Gary Green 31 Jan '08

31 Jan '08

---------------------------- Plastic bags and paper work have been left on the bed in the MRI corridor. Please ensure that your projects are aware that this is a clinical area and needs to remain clean and tidy. Will you please also remind students that any scrubs worn need to be put in the laundry bin. Thank you

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[Fwd: [Staff] MRI corridor]
by a.morland＠psychology.york.ac.uk 31 Jan '08

31 Jan '08

Dear All, I am copying Claire's message to all users, so that everyone is aware of the need to keep the MRI corridor clear of debris. Thanks Tony ---------------------------- Original Message ---------------------------- Subject: [Staff] MRI corridor From: "Claire Fox" <claire.fox(a)ynic.york.ac.uk> Date: Thu, January 31, 2008 10:06 am To: staff(a)ynic.york.ac.uk -------------------------------------------------------------------------- Plastic bags and paper work have been left on the bed in the corridor. Please ensure that your projects are aware that this is a clinical area and needs to remain clean and tidy. Will you please also remind students that any scrubs worn need to be put in the laundry bin. Thank you Claire _______________________________________________ Staff mailing list Staff(a)ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/staff

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masterclasses: MSc commitments
by Andre Gouws 29 Jan '08

29 Jan '08

I would like to re-iterate (see my previous email of 21/01/08): "MSc students with timetable commitment that prevent them attending the masterclasses should be aware that it is our intention to run a separate session(s) for the MSc program. (Date to be confirmed)." Sylvia - we are happy to liaise with you on this. ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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MRI masterclass - split session - Thursday 31st January
by andre＠ynic.york.ac.uk 28 Jan '08

28 Jan '08

Thank you to those of you who replied to my previous emails requesting that you contact us if you intend to attend any/all of the current masterclasses. We have had a low response in terms of attendance for this week's MRI session (so far only 5 interested parties). Those 5 five will be glad to know that we fully intend to continue with the session - the tutorials will be even more interactive than usual if the numbers are smaller! However, it would be naive of me to ignore the feedback from some that suggests that committing 2 1/2 hours on a Thursday afternoon is difficult for some of you. As such a minor revision to Thursday's program is proposed: The session will be split into 2 halves - Session 1: 2.30 - 4.00 - an introduction to the FSL software environment; - a full single subject AND across subject (group) fMRI analysis tutorial with worked examples; - examples of manipulating data - co-registration, averaging, extracting time-series (with user supplied examples), extracting brains Session 2: 4.00 - 5.00 - an introduction to the more weird and wonderful tools in fsl - exploring fMRI data without a model .. ICA - comparing spatial differences between groups - TBSS and VBM - exploring connectivity with DTI data - again, session will involve worked examples and user interaction with scripts Hopefully splitting the session will help those of you limited by time to attend at least part of the afternoon, and allow those of you who are only interested in basic fMRI processing / newer features to attend the times most suitable for you. Please do let us know if you intend to attend .. it makes our lives easier! Thanks. ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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MEG
by Gary Green 22 Jan '08

22 Jan '08

You will all be pleased to hear that we now have a certificate that states that the oxygen level in MEG is 20.9% The oxygen monitor has also been shown to detect and alarm when the level is low (18%). What this really means is that the oxygen monitor has been calibrated. It is now safe to scan again in MEG Thanks to 4D Neuroimaging, Joanna and Maribel who help sort this out so quickly Gary -- Gary Green Director 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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Masterclasses - register
by Andre Gouws 21 Jan '08

21 Jan '08

MSc students with timetable commitment that prevent them attending the masterclasses should be aware that it is our intention to run a separate session for the MSc program. (Date to be confirmed). -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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Masterclasses - register
by Andre Gouws 21 Jan '08

21 Jan '08

FYI: Masterclasses are 2 and a half hour interactive tutorial sessions which start at 2:30 pm. -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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Masterclasses - register
by Andre Gouws 21 Jan '08

21 Jan '08

To give us an indication of the type of numbers we can expect at the forthcoming masterclasses, please reply to this email if you intend to attend the following sessions (and indicate which you will attend): Thursday 24th Jan - Visualisation tools Thursday 31st Jan- MRI tools Thursday 7th Feb - MEG tools Thanks -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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Virtual electrodes as a YNiC Analysis Support Colloquium?
by Andy Ellis 18 Jan '08

18 Jan '08

Piers and I would be willing to attempt to lead one or two sessions on virtual electrode analysis in MEG. Points for discussion could include: 1. Where you can stick your virtual electrodes. How to position your VEs to best effect. 2. What kinds of information you can get out of VEs - analyses in the frequency and amplitude domains. 3. What kinds of statistical analyses would it be good to be able to do? These might best be done after the MEG masterclass on 7 Feb. Any interest? Andy >Delivered-To: psychology.york.ac.uk-a.ellis(a)psych.york.ac.uk >Date: Thu, 17 Jan 2008 17:35:35 +0000 >From: Michael Simpson <michael.simpson(a)ynic.york.ac.uk> >To: ynic-users(a)ynic.york.ac.uk >Subject: YNiC Analysis Support Colloquia >X-BeenThere: ynic-users(a)ynic.york.ac.uk >List-Id: YNiC user discussion list <ynic-users.ynic.york.ac.uk> >List-Unsubscribe: <https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users>, > <mailto:ynic-users-request@ynic.york.ac.uk?subject=unsubscribe> >List-Archive: <https://www.ynic.york.ac.uk/mailman/private/ynic-users> >List-Post: <mailto:ynic-users@ynic.york.ac.uk> >List-Help: <mailto:ynic-users-request@ynic.york.ac.uk?subject=help> >List-Subscribe: <https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users>, > <mailto:ynic-users-request@ynic.york.ac.uk?subject=subscribe> >X-York-MailScanner: Found to be clean >X-York-MailScanner-From: ynic-users-bounces(a)ynic.york.ac.uk > >Dear Users, > >YNiC would like to invite you to the YNiC Analysis Support Colloquia. >These sessions will take place on Wednesday evenings from 4pm to 5pm in >Room B020, Psychology. This new session is designed to get Users to >present and discuss contemporary analysis problems. They are open to all >Users, and will be attended by as many YNiC staff as are available. > >The format will be: > > * A User will send a message to ynic-users(a)ynic.york.ac.uk to say >that they would like to have a YNiC ASC on a set date, and on a set subject. > > * Once a User has nominated a particular date, they are effectively >the chair for that session. Before the session, the chair will be >expected to forward an agenda to the User list to let YNiC staff, and >Users, know what the topic of the session will be, and who will present >what. > > * The chair will be expected to make a short presentation on an >analysis problem at their YNiC ASC, and then lead the subsequent discussion. > > * If another User would like to present at a colloquia that is >already being chaired, it will be up to the User to contact the chair in >advance to see if their data / problem is appropriate for the session. >Therefore, in some colloqiua there may be more than one example of the >problem presented. > > * The chair for the session may be asked to add to the YNiC >documentation after their session if new insights into analyses have >been gleaned. > >Those of you who have had a brainstorm will recognise aspects of the >format. The new YNiC ASC will hopefully open these brainstorms up so >that all Users can benefit from them. Hence, analysis insights that >emerge form these colloquia will be open to the whole User community. >These colloquia will also replace interpretation support that may >previously have been available via your SLO. This has been decided to >ensure that all projects have the potential for the same support, and >also that all projects will essentially benefit from input from all YNiC >staff and Users, rather than just one individual. We hope that it will >be a self-supporting enterprise for the whole User community. (N.B. Note >that technical support related to your analysis will still be available >from your SLO.) > >So, all that is left to do is email ynic-users(a)ynic.york.ac.uk and >volunteer for a YNiC ASC, making sure to state the date and subject. > >Best Wishes, >Michael > >P.S. We appreciate that there may be occasions when there is a clash >with Board of Studies meetings however, as there is only 2 per term, >this will only be problem 6 times a year. On these occasions Users can >suggest to the chair of the YNiC ASC that they might move their date to >another day. Alternatively, there may be very specific or technical >problems that might be appropriate for a YNiC ASC that clashes with a >Board of Studies meeting. > >-- >Dr Michael Simpson >Science Liaison Officer >York Neuroimaging Centre >Innovation Way >York >YO10 5DG > >Tel: 01904 567614 >Web: http://www.ynic.york.ac.uk > >-- >ynic-users mailing list >ynic-users(a)ynic.york.ac.uk >https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users -- 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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YNiC Analysis Support Colloquia
by Michael Simpson 17 Jan '08

17 Jan '08

Dear Users, YNiC would like to invite you to the YNiC Analysis Support Colloquia. These sessions will take place on Wednesday evenings from 4pm to 5pm in Room B020, Psychology. This new session is designed to get Users to present and discuss contemporary analysis problems. They are open to all Users, and will be attended by as many YNiC staff as are available. The format will be: * A User will send a message to ynic-users(a)ynic.york.ac.uk to say that they would like to have a YNiC ASC on a set date, and on a set subject. * Once a User has nominated a particular date, they are effectively the chair for that session. Before the session, the chair will be expected to forward an agenda to the User list to let YNiC staff, and Users, know what the topic of the session will be, and who will present what. * The chair will be expected to make a short presentation on an analysis problem at their YNiC ASC, and then lead the subsequent discussion. * If another User would like to present at a colloquia that is already being chaired, it will be up to the User to contact the chair in advance to see if their data / problem is appropriate for the session. Therefore, in some colloqiua there may be more than one example of the problem presented. * The chair for the session may be asked to add to the YNiC documentation after their session if new insights into analyses have been gleaned. Those of you who have had a brainstorm will recognise aspects of the format. The new YNiC ASC will hopefully open these brainstorms up so that all Users can benefit from them. Hence, analysis insights that emerge form these colloquia will be open to the whole User community. These colloquia will also replace interpretation support that may previously have been available via your SLO. This has been decided to ensure that all projects have the potential for the same support, and also that all projects will essentially benefit from input from all YNiC staff and Users, rather than just one individual. We hope that it will be a self-supporting enterprise for the whole User community. (N.B. Note that technical support related to your analysis will still be available from your SLO.) So, all that is left to do is email ynic-users(a)ynic.york.ac.uk and volunteer for a YNiC ASC, making sure to state the date and subject. Best Wishes, Michael P.S. We appreciate that there may be occasions when there is a clash with Board of Studies meetings however, as there is only 2 per term, this will only be problem 6 times a year. On these occasions Users can suggest to the chair of the YNiC ASC that they might move their date to another day. Alternatively, there may be very specific or technical problems that might be appropriate for a YNiC ASC that clashes with a Board of Studies meeting. -- 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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Seminar today at YNiC
by Gary Green 17 Jan '08

17 Jan '08

The first of the 2008 seminars at YNiC as advertised on the web site at https://www.ynic.york.ac.uk/events/ynic-thursday-seminars will be today at 4pm in the YNiC open plan area "1. The new software and documentation" a presentation led by the YNiC team Refreshments will be available afterwards This is followed in the next few weeks by masterclasses that go through the practical aspects of the new software and documentation in detail. 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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Might be of interest
by Philip Quinlan 02 Jan '08

02 Jan '08

Quite an interesting paper has just appeared in Perspectives on Psychological Science 2,(4), Dec 2007 - A trio of concerns by Jerome Kagan. Includes some interesting observations on the differences between MEG and MRI. Enjoy. PQ. -- ******************************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 433181 University of York Tel: (01904) 430000 Ext. 3135 Heslington Direct : (01904) 433135 York Telex: 57933 YORKUL YO10 5DD U.K. ********************************************************************************

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showcase
by Gary Green 20 Dec '07

20 Dec '07

Just to note, that as there are hardly any people around at the moment, we have postponed the poster afternoon until later in 2008 -- 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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Christmas Drinks and Mince Pies
by Gary Green 20 Dec '07

20 Dec '07

You are cordially invited to partake of mince pies and drinks at YNiC at 4pm today -- 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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Seminar today
by Gary Green 13 Dec '07

13 Dec '07

This afternoon's seminar is a new project presentation "Functional imaging with hyperpolarised carbon dioxide" 4pm, ynic open plan all welcome -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

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HBM-travel awards
by Cindy Hagan 12 Dec '07

12 Dec '07

On a related note, grad students and post-docs can apply for a $750 travel bursary. It's not much money (especially with the ever-declining value of the USD) but better than paying the entire £760 airfare yourself! Deadline is April '08. See link below: http://ric.uthscsa.edu/hbmtravelawards/ Cindy

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Human Brain Mapping Conference
by Gary Green 12 Dec '07

12 Dec '07

The deadline for submitting an abstract for HBM is fast approaching (January 6th 2008). Details can be obtained from https://www.ynic.york.ac.uk/user-resources/conferences-and-abstract-deadlin… and http://www.hbm2008.com/ Why not join me in Melbourne 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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MRI operator training
by rem 10 Dec '07

10 Dec '07

Dear YNiC Users Users are invited to take part in an MRI operator training course held at YNiC. Clinical scanning is currently placing a high demand on the MRI facilities. To provide more flexibility for MRI research scanning, especially for unfunded projects, we would like to encourage Users to become MRI operators so that they can collect their own data during off-peak hours (after 5 pm). At this point please could you let me know if you, or other members of your research team, are interested in becoming MRI operators. Once we have an idea of numbers, we will plan a training schedule that will be as convenient as possible for everyone involved. N.B. 1) MRI operators must have a valid first aid certificate. You need to have a first aid certificate before you are allowed to operate the MRI scanner independently. 2) Two qualified MRI operators must be present for out-of-hours scanning. Therefore you will need to train at least two members of your research team, or co-ordinate your scanning with other qualified MRI operators. Best wishes Rebecca -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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Tonight at YNiC
by Gary Green 06 Dec '07

06 Dec '07

Dear users Tonight is the first of our roundtable discussions on the future at ynic. The topic is 'eye-tracking' Andy Ellis will lead the discussion but contributions/presentations from others are welcome. The aim of these roundtables is to discuss what/why/how/when we might attempt to address a particular need within the user community at YNiC. 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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Human Brain Anatomy Course
by Uzma Urooj 05 Dec '07

05 Dec '07

FYI. It may be of interest to some of you. They also have a summer session for this course. Uzma Human Brain Anatomy Course 2nd-4th April 2008 Venue: Institute of Child Health Suitable for undergraduates/postgraduates in neuroscience, medicine and psychology. - 3-day programme, assumes minimal prior knowledge - emphasises functional and clinical neuroanatomy - includes dissecting-room sessions examining real brains! _ __http://www.neurocourses.com/_

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MEG talk today
by Shane Lindsay 03 Dec '07

03 Dec '07

Dear all, Today's Psycholinguistics Research Meeting meeting is going to be held in A202, at 12.30. Our guest is 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. Best, Shane

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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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