ynic-users

ynic-users@ynic.york.ac.uk

2 participants
2817 discussions

Seminar at YNiC Wednesday 2nd May 12-1pm
by a.morland＠psychology.york.ac.uk 23 Apr '07

23 Apr '07

Holly Bridge, Dorothy Hodgkin Fellow, University of Oxford will be talking on the following at YNiC. Combining diffusion-weighted and functional MRI to investigate normal and abnormal human visual cortex Time: 12-1pm Date: 2nd May Cheers Tony

1 0

Staff Cricket
by Michael Simpson 23 Apr '07

23 Apr '07

Dear all, I now have the application form for the staff cricket league, and will be about to enter a team into it for Psychology. As stated in previous mailings, there will be approximately 10 games between mid May and the end of August, all starting at 5.30 on the Oak Tree pitches (almost opposite Psychology ... ). The matches are friendly in nature and cater for all abilities. Novices welcome, the only criteria is that you are either Uni staff or post-graduate. Rather than persistently cross-post throughout the summer, I'd like to set up a mailing list for interested parties. So, if you're interested in being kept informed of practices and games, please reply to me and I'll generate an email list. I don't mind whether your interested is at the level of spectating, playing a few games or stalwart; it'd just be good to collate a list of interested parties. The names that will automatically be added, as they've already shown (some) level of interest are: Me, Tony Morland, Tim Andrews, Andre Gouws, Sam Johnson, Gary Green, Garreth Prendergast, Philip Quinlan, Padraic Monaghan, Peter Thompson, Phil Pell, Tom Hartley, Andy Ellis, Martin Edmundson, Sam Gardiner, Tom Hartley, Padraig Kitterick, Richard Allen. Hopefully there will be an outdoor net session either next week or the week after. I'll let you know when I know. With 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

1 0

Thursday 26th April - YNiC Seminar
by Michael Simpson 23 Apr '07

23 Apr '07

Dear all, Its a new term and the YNiC Thursday evening Seminars are back! Usual time, 4pm in YNiC Open Plan. The new timetable of talks will be presented and discussed on Thursday evening. However, in the timetable will be a series of talks where YNiC Users feedback to the YNiC User community from their Brainstorm sessions. The idea is that they will present a similar presentation to what they presented at their Brainstorm, discuss the problems that were highlighted, and then present their subsequent findings. Hopefully, these presentations will be of interest to all YNiC Users. First up this Thursday (26th April), is Laura Barca with her presentation: "My experiences with Virtual Electrodes: Feedback from a YNiC Brainstorm." With 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

1 0

MRI scanning procedures
by a.morland＠psychology.york.ac.uk 23 Apr '07

23 Apr '07

Dear All, [Sorry for cross postings] Apologies for the long message, but please read it carefully because it contains information concerning MRI scanning. YNiC now has a new radiographer, Chris Alderson, who has extensive experience of MRI scanning. She is however new to the research environment and will therefore be in need of support from researchers using the scanner. With this is mind this seems like a good opportunity to remind investigators of the following. 1) Scanning Protocols Please be sure that you know the scanning protocols that you will be using. In many circumstances your protocols are saved on the scanner in a project folder named with your project number (e.g. P1025). If you do not know your protocols, please get in touch with your SLO so that we can prepare a scanning protocol for you. If you are obtaining structural scans as part of an MEG study, there is already a predefined protocol that Chris is aware of. 2) Stimulus arrangements It is also essential that you are able to present your stimuli without assistance from Chris. You will also need to be able to give clear instructions to Chris about when she should commence scanning with respect to stimulus onset etc. You are, of course, able to liaise with your SLO if you need help. 3) Timeliness As a courtesy to Chris, please ensure that you and your participants arrive promptly for your scanning session. Also, be sure to book the appropriate amount of time for your scan session. This is likely to become increasingly important as non-research clinical scanning picks up, because we will be unable to have research time overrun to displace or delay fee paying clinical scanning. 4) Participant preparation It is the investigators responsibility to have their participants prepared for the scan and prepared on time. This means that participants need to be registered for the scan and appropriately dressed. Participants are able to wear gowns if they clothing is not suitable for scanning. Chris is responsible for a final screening of the participant and will take them into the exam room. 5) Access to corridor, console room and exam room. Only investigators who have been named as such may be present in the console room during scanning. Participants should be prepared for scanning in the corridor, where changing facilities and lockers for valuables are available and should be used. Once the participant is ready, only the investigator should enter the console room to let Chris know that the participant is ready. Chris will then invite the participant to come through to the console room, where she will perform final checks, and then take them through to the exam room. Please keep the number of investigators in the console to a minimum. Please note that as the centre becomes busier (as anticipated) adhering to the above with become increasingly more important. If you are unsure about anything raised in this message, please feel free to get in touch with me, Andre Gouws or your SLO. Thanks Tony

1 0

Cricket nets
by Michael Simpson 13 Apr '07

13 Apr '07

Dear all, We are going to try and have one more indoor cricket net before the end of Easter. From asking those who were at the last net, the best time would be next Wednesday. However, at 6 - 7 pm two of the four nets are booked for Universtiy staff. Before and after they are usually full for Badminton. Depending on interest, you would all be welcome to attend the staff nets. I go regularly. However, if there are a number of us it may be polite to book an extra net or two for our own use. Also, if you are a novice but keen, I'll make sure I book an extra net so that batting is an enjoyable rather than intimidating experience! Let me know what the interest is so I can book the nets accordingly, thanks, Michael P.S. I'll book an outdoor net in a few weeks time. -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

1 0

Thursday Seminar
by Sam Johnson 29 Mar '07

29 Mar '07

Hello all, It seems that people are beginning to drift away for Easter, so there will be no Thursday afternoon session this week. There will be mails over the next couple of weeks setting out the plan for next term, and asking for volunteers to lead some sessions. Thanks, Sam

1 0

Meeting @ Brunel 2nd April
by a.morland＠psychology.york.ac.uk 28 Mar '07

28 Mar '07

----------------------------------------------------------- - Meeting Announcement (apologies for any cross-postings) - Monday 2nd April 2007 The Centre for Cognition and Neuroimaging at Brunel University is hosting a one-day symposium entitled "New Directions in Cognitive Neuroscience", which will have a particular focus on neuroimaging and electrophysiology. Confirmed speakers include: Prof. Larry Parsons (University of Sheffield, UK) Prof. Riitta Salmelin (Helsinki University of Technology, Finland) Prof. Masud Husain (Institute of Cognitive Neuroscience, UK) Prof. Olaf Blanke (Brain-Mind Instiute, Switzerland) Prof. Beatrice de Gelder (Tilburg University, The Netherlands) Prof. Andy Smith (Royal Holloway, UK) The symposium is an open meeting and registration is free but mandatory. A buffet lunch and refreshments are included. Note that places are limited, so please book in advance. Poster contributions are welcome - please e-mail an abstract of no more than 250 words to michael.wright(a)brunel.ac.uk More details may be found at http://www.brunel.ac.uk/cogneuro We look forward to seeing you at the meeting! --- Noam Sagiv - Andrew Parton - Maria Uther Adrian Williams - Michael Wright - Taeko Wydell

1 0

Cricket Nets
by Michael Simpson 23 Mar '07

23 Mar '07

Dear all, as mentioned last year, I am intending to enter a Psychology team into the inter-departmental 'Tinpot' cricket tournament this summer. This is a 'no experienced needed' cricket league, with most departments entering teams that have a combination of experienced and inexperienced players. The only inclusion criteria is that you are Staff or on a postgraduate course, i.e. PhD, MSc. There are 9 - 10 matches between May and August, timed not to coincide with graduation and exams etc. There is a nucleus of a team that has formed at YNiC, but we need more players. We are having an indoor net next Thursday at 6pm, after the Thursday evening seminar at YNiC. No ability needed, after all, I'll be playing ... Please let me know if you are interested to come along. At the moment I've only booked one net, but we can book another if necessary. Also, if you have any kit, including any cricket balls, they'd be welcome (as we have to provide our own kit for indoor nets). If you are interested and can't make it, we'll try and organise some outdoor nets, or a friendly game, before the season starts. However, since the students are on holiday, we thought we'd exploit the availability of the indoor nets now. Best wishes, 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

1 0

Thursday Evening
by Sam Johnson 07 Mar '07

07 Mar '07

Hello all, As part of the revamped Thursday afternoon sessions, at 4pm tomorrow there will be project presentations from people planning studies at YNiC. The following Thursday, the 15th, Andre will be demonstrating some of the features of his new visualisation tool. The intention of these sessions is to encourage dialog so that the whole YNiC user community, including YNiC staff, can share the benefits of their experiences and expertise. As such these sessions will take a variety of forms; journal clubs, project presentations, progress reports, seminars, training and so on. In the near future there will be "friendly" requests for investigators involved in projects to prepare informal progress reports, but in the mean time please do come along and partake of some wine and snacks and see what other people are planning. Thanks Sam

1 0

MRI data processing
by Mark Hymers 05 Mar '07

05 Mar '07

Hi, As some of you will know, due to an interesting issue [0] caused by GE installing an MRI scanner update, we have been having some problems with transferring and processing MRI data recently. Because GE (despite having admitted that this is their fault) are unable to fix this in a timely manner, we've now managed to work around it in house and have processed the backlog of data. Everything up until last week has now been processed and uploaded and last weeks' scans will be processed by the end of today. Apologies for the delay but this came out of nowhere and even diagnosing the problem took quite a bit of time. If anybody thinks that scans they have performed since the start of the year have not been processed, can you please send an email to mri-support(a)ynic.york.ac.uk with details and we'll look into it. Cheers, Mark [0] For Those Who Care About Technical Details The executive summary is that they've changed the two values which represent the Minimum (0028,0108) and Maximum (0028,0109) pixel values in the image from 16 bit signed to 16 bit unsigned. The data which is exported is still 16 bit signed and so this change makes absolutely no sense whatsoever. Quite a bit of DICOM code I've looked at will cope with either US or SS for these values but expects them to be consistent with the actual data (which makes sense, if you're expressing a minimum or maximum, it should be done using the same data type as the data). A full dissection of the problem follows: Old DICOM Image (selected tags only): (0028,0103) US 1 # 2, 1 PixelRepresentation (0028,0106) SS 0 # 2, 1 SmallestImagePixelValue (0028,0107) SS 275 # 2, 1 LargestImagePixelValue New DICOM Image (selected tags only): (0028,0103) US 1 # 2, 1 PixelRepresentation (0028,0106) US 0 # 2, 1 SmallestImagePixelValue (0028,0107) US 2211 # 2, 1 LargestImagePixelValue As you can se from the second column, the two bottom tags have changed their Value Representation from SS (Signed Short) to US (Unsigned Short). I've included the tag (0028,0103) because it explains how the actual pixel data is to be interpreted. MR is fixed at 16 bits which leaves two options: signed (2's complement) and unsigned. To quote from the DICOM Standard: Pixel Representation (0028, 0103): Data representation of the pixel samples. Each sample shall have the same pixel representation. Enumerated values: 0000H = unsigned integer 0001H = 2's complement So, the data is still written as signed, whilst the min and max values are written as unsigned. This is, at least in spirit if not letter, a violation of the DICOM standard. Note that although I state that according to the DICOM spec, MR is fixed at 16 bits, the interpretation of those 16 bits isn't fixed. See the tags BitsStored, BitsAllocated and HighBit if you're interested. (In practice, this is usually fixed for MR at 16, 16 and 15 respectively). The fix is to read the value out of the file and hack the relevant VRs back to being a signed integer instead of an unsigned one. The interesting thing is that images processed with Clariview (e.g. the YNiC Structurals which have FL_E in them) still use the signed value. So not only are GE wrong, they're inconsistently wrong too. -- Mark Hymers York Neuroimaging Centre

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users