ynic-users March 2007

ynic-users@ynic.york.ac.uk

5 participants
5 discussions

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

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users March 2007