Difference: ProjectsCCPPETMR (1 vs. 17)

Revision 1710 Aug 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET-MR)

Line: 72 to 72
  Setup and access to web-site (potentially just IP address access to put some content on there), mailing lists etc.
Changed:
<
<
The PET reconstruction engine will initially be based on STIR, http://stir.soruceforge.net. Need to merge in a few local branches first (e.g. clean-up of GE contributed code) before open git access.
>
>
The PET reconstruction engine will initially be based on STIR, http://stir.sourceforge.net. Need to merge in a few local branches first (e.g. clean-up of GE contributed code) before open git access.
  For MR, we will this year (2015-2016) target the Gadgetron. http://gadgetron.github.io/

Revision 1609 Jul 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
Changed:
<
<

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

>
>

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET-MR)

  The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.
Line: 31 to 31
 
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London. We had 19 attendants from academia, representing all the UK groups working on (or interested in) PET-MR data processing and 5 attendants from industry (GE, Imanova, Philips, Siemens). Presentations, minutes etc are available from the main website http://www.ccppetmr.ac.uk/ (Working Group tab)

p2015-05-13_onep40w.jpg

Deleted:
<
<

 
  • CCP SP at Daresbury Labs 24 June 2015

Revision 1527 Jun 2015 - KrisThielemans

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 21 to 21
  There is a JISCMAIL list at: https://www.jiscmail.ac.uk/CCP-PETMR easy to sign up by following this link.
Changed:
<
<
There is an email for information: ccppetmr@stfc.ac.uk
>
>
There is an email for information: ccppetmr at stfc.ac.uk
 

Events

  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
  • Meetings of Executive Committee to assign tasks and prepare Working Group meeting are ongoing
  • 27-30 April 2015 Physics & Software PET-MR training school in Leeds. Together with the EU COST action TD1007: "Bimodal PET-MRI molecular imaging technologies and applications for in vivo monitoring of disease and biological processes", we co-organised and co-sponsored the 2nd International Training School on PET-MRI Engineering. This 4 day school was attended by 33 trainees (9 from the UK). http://www.pet-mri.eu/PETMR_School_15.html
Changed:
<
<
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London. We had 19 attendants from academia, representing all the UK groups working on (or interested in) PET-MR data processing and 5 attendants from industry (GE, Imanova, Philips, Siemens).
>
>
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London. We had 19 attendants from academia, representing all the UK groups working on (or interested in) PET-MR data processing and 5 attendants from industry (GE, Imanova, Philips, Siemens). Presentations, minutes etc are available from the main website http://www.ccppetmr.ac.uk/ (Working Group tab)
  p2015-05-13_onep40w.jpg
Changed:
<
<
Presentations: Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf
>
>

 
  • CCP SP at Daresbury Labs 24 June 2015
Line: 45 to 44
  Developer’s Meetings:
Changed:
<
<
  • July 2015: software design of overarching framework
>
>
  • Tuesday 7th of July 2015 (1-5pm at UCL): software design of overarching framework
 
  • September 2015: Training: Software Carpentry (git, compiling, good programming practices)
  • November 2015: framework update and first release preparation
Line: 74 to 73
  Setup and access to web-site (potentially just IP address access to put some content on there), mailing lists etc.
Changed:
<
<
The PET reconstruction engine will initially be based on STIR, with git access available. Need to merge in a few local branches first (e.g. clean-up of GE contributed code) before open access.
>
>
The PET reconstruction engine will initially be based on STIR, http://stir.soruceforge.net. Need to merge in a few local branches first (e.g. clean-up of GE contributed code) before open git access.
 
Changed:
<
<
For MR, we will this year (2015-2016) target the Gadgetron. http://gadgetron.github.io/ Experience and need to check out facilities etc.
>
>
For MR, we will this year (2015-2016) target the Gadgetron. http://gadgetron.github.io/
  For both, our intention is to create a user-friendly level "above" these such that at later stage we can add support for other packages. The super-level will need to have MATLAB support. It's still unclear if other target languages are desired. It could be that we create the "super-level" in C++, and then use SWIG to provide the MATLAB/Python/etc interface for instance.
Changed:
<
<
Regarding SWIG. As I mentioned, "mainline" SWIG doesn't have any MATLAB support yet. This work was started by someone as a Google Summer of Code project in 2009 or so. It was then last year taken up by someone called Joel Andersson, and I helped taking it forward. It seems to have stalled a bit again. F ork from KT is on https://github.com/KrisThielemans/swig

"This is the one that at UCL we are currently using for creating MATLAB support for STIR. Joel's is on https://github.com/jaeandersson/swig he's a bit ahead of me now. He merged some things from master back in and made a few small updates. I expect that would work for us without trouble, but haven't tried yet (and there's no good test-suite yet). Joel's behind master again, but again I don't think that matters too much (because SWIG supports a lot of languages, there are a lot of updates that are irrelevant to the MATLAB side of things. The "core" itself of SWIG doesn't change a lot)."

"Brief summary of current status of MATLAB support in SWIG:

>
>
Regarding SWIG. "mainline" SWIG doesn't have any MATLAB support yet but good progress is being made https://github.com/jaeandersson/swig. A fork from KT is on https://github.com/KrisThielemans/swig works for adding MATLAB support to STIR. Brief summary of current status of MATLAB support in SWIG:
  - a lot of things work. It works for STIR, and STIR is relatively complicated.
Line: 96 to 91
  - the SWIG maintainers rightly insist on the test-suite to work, and having TRAVIS support. The latter is tricky as TRAVIS doesn't have MATLAB (no license). There has been some discussion on getting minimal "run swig + compile" support for this on TRAVIS (i.e. without running the tests in MATLAB).
Changed:
<
<
I suggest that most "general" communications on SWIG happen via the SWIG-devel mailing list, as we don't want to solve this on our own. A relatively old post is for instance, http://swig.10945.n7.nabble.com/SWIG-for-MATLAB-An-update-and-call-for-collaboration-td13950.html "
>
>
For conversations on SWIG, we will use the SWIG-devel mailing list, as we don't want to solve this on our own. A relatively old post is for instance, http://swig.10945.n7.nabble.com/SWIG-for-MATLAB-An-update-and-call-for-collaboration-td13950.html.
 
Changed:
<
<
I think we should use the STIR mailing lists for anything that applies to the general STIR audience. That way, we hopefully will get some help from the international community as well (and relief some of the pressure on me). STIR mailing list info is on the STIR website.
>
>
We should use the STIR mailing lists for anything that applies to the general STIR audience. That way, we hopefully will get some help from the international community as well (and relief some of the pressure on me). STIR mailing list info is on the STIR website.
 

Contacts:

Changed:
<
<
Kris Thielemans: k.thielemans@ucl.ac.uk
>
>
Kris Thielemans: k.thielemans at ucl.ac.uk
 
Changed:
<
<
Ron Fowler: ronald.fowler@stfc.ac.uk
>
>
Ron Fowler: ronald.fowler at stfc.ac.uk
 
Changed:
<
<
Martin Turner: martin.turner@stfc.ac.uk
>
>
Martin Turner: martin.turner at stfc.ac.uk
  -- MartinTurner - 10 Feb 2015
Added:
>
>
-- KrisThielemans - 27 Jun 2015
 
META FILEATTACHMENT attachment="05484183.pdf" attr="" comment="" date="1428482542" name="05484183.pdf" path="05484183.pdf" size="968059" stream="05484183.pdf" tmpFilename="/tmp/U5SvDC4XAI" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482639" name="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="624041" stream="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/IDfdQzbWQL" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482720" name="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="1151084" stream="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/cUyGCkjEXo" user="MartinTurner" version="1"

Revision 1425 Jun 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.

Changed:
<
<
This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
>
>
This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020: with official website at: http://www.ccppetmr.ac.uk/
  The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)
Line: 19 to 19
 

Mailing List

Changed:
<
<
There is a JISCMAIL list at: https://www.jiscmail.ac.uk/CCP-PETMR

Easy to sign up by following this link.

>
>
There is a JISCMAIL list at: https://www.jiscmail.ac.uk/CCP-PETMR easy to sign up by following this link.
  There is an email for information: ccppetmr@stfc.ac.uk
Line: 34 to 32
  p2015-05-13_onep40w.jpg
Changed:
<
<
Presentations:

Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf

>
>
Presentations: Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf
 
  • CCP SP at Daresbury Labs 24 June 2015

Revision 1324 Jun 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 23 to 23
  Easy to sign up by following this link.
Added:
>
>
There is an email for information: ccppetmr@stfc.ac.uk
 

Events

  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
Line: 35 to 37
 Presentations:

Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf

Added:
>
>
  • CCP SP at Daresbury Labs 24 June 2015
 
Future Events:

UK workshops:

Revision 1217 Jun 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 6 to 6
  This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
Changed:
<
<
The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews\x{200e} (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)\x{200e}
>
>
The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)
  This collaborative computational project (CCP) in synergistic PET-MR image reconstruction has two primary aims:
Line: 26 to 26
 

Events

  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
Changed:
<
<
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
  • Presentations from the train school may be made available on this wiki or the website.
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London.
>
>
  • Meetings of Executive Committee to assign tasks and prepare Working Group meeting are ongoing
  • 27-30 April 2015 Physics & Software PET-MR training school in Leeds. Together with the EU COST action TD1007: "Bimodal PET-MRI molecular imaging technologies and applications for in vivo monitoring of disease and biological processes", we co-organised and co-sponsored the 2nd International Training School on PET-MRI Engineering. This 4 day school was attended by 33 trainees (9 from the UK). http://www.pet-mri.eu/PETMR_School_15.html
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London. We had 19 attendants from academia, representing all the UK groups working on (or interested in) PET-MR data processing and 5 attendants from industry (GE, Imanova, Philips, Siemens).
  p2015-05-13_onep40w.jpg

Presentations:

Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf

Added:
>
>
Future Events:

UK workshops:

  • Q4 2015: 1-day workshop jointly organised with CCPi: Synergistic Reconstruction of Multi-modality and/or Multi-spectral data
  • Q2 2016: 2-day workshop: Issues in PET-MR Reconstruction and Quantification (educative sessions, software training, research presentations)

Developer’s Meetings:

  • July 2015: software design of overarching framework
  • September 2015: Training: Software Carpentry (git, compiling, good programming practices)
  • November 2015: framework update and first release preparation

International activities:

  • Nov 2015: STIR User’s Meeting at IEEE Medical Imaging Conference
  • Nov 2015: Satellite Workshop at IEEE Medical Imaging Conference Open Source Software in Medical Imaging
 

Reading Materials

Revision 1127 May 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 6 to 6
  This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
Changed:
<
<
The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews‎ (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)‎
>
>
The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews\x{200e} (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)\x{200e}
  This collaborative computational project (CCP) in synergistic PET-MR image reconstruction has two primary aims:
Line: 27 to 27
 
  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
Changed:
<
<
  • Presentations from the train school are now available here: PetMr_talks
>
>
  • Presentations from the train school may be made available on this wiki or the website.
 
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London.

p2015-05-13_onep40w.jpg

Revision 1022 May 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 27 to 27
 
  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
Added:
>
>
  • Presentations from the train school are now available here: PetMr_talks
 
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London.

p2015-05-13_onep40w.jpg

Revision 921 May 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 8 to 8
  The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews‎ (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)‎
Added:
>
>
This collaborative computational project (CCP) in synergistic PET-MR image reconstruction has two primary aims:

1) PET-MR Networking

The UK has a number of research groups with high international standing, working on image reconstruction and analysis for either PET or MR. We aim to bring these groups together towards the goal of synergistic PET-MR image reconstruction and analysis by advancing understanding of PET-MR and the algorithms used for each modality. We will foster links with the wider international PET and MR communities to further achieve this goal.

2) Developing PET-MR Software Infrastructure

We aim to provide enabling infrastructure for research in PET-MR by development and promotion of a common software framework to tackle the specific challenges of PET-MR imaging. This will be achieved by standardisation of data formats, creating tools to export data in these data formats and development of a software platform for integrated PET-MR image reconstruction.

 

Mailing List

There is a JISCMAIL list at: https://www.jiscmail.ac.uk/CCP-PETMR

Line: 16 to 25
 

Events

Changed:
<
<
  • Initial kick-off meeting with the CoIs on the 1st of April at UCL
>
>
  • Initial kick-off meeting with the CoIs was held on the 1st of April at UCL
 
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
Changed:
<
<
  • Initial meeting with the Working Group has been arranged for the 13th May 2015 11:30 to 15:00 at St Thomas Hospital, London.
>
>
  • Initial meeting with the Working Group was held on the 13th May 2015 11:30 to 15:00 at St Thomas' Hospital, London.

p2015-05-13_onep40w.jpg

Presentations:

Martin J. Turner - STFC/SCD facilities and new CCP plans - corefunctions_c.pdf

 

Reading Materials

Line: 80 to 95
 
META FILEATTACHMENT attachment="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482639" name="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="624041" stream="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/IDfdQzbWQL" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482720" name="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="1151084" stream="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/cUyGCkjEXo" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="CPP-logo2-DokChampa-cropped.png" attr="" comment="" date="1432051796" name="CPP-logo2-DokChampa-cropped.png" path="CPP-logo2-DokChampa-cropped.png" size="13758" stream="CPP-logo2-DokChampa-cropped.png" tmpFilename="/tmp/l0yPb8curL" user="RonFowler" version="1"
Added:
>
>
META FILEATTACHMENT attachment="p2015-05-13_onep40w.jpg" attr="" comment="" date="1432234439" name="p2015-05-13_onep40w.jpg" path="p2015-05-13_onep40w.jpg" size="20060" stream="p2015-05-13_onep40w.jpg" tmpFilename="/tmp/Eevj1jmx3M" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="corefunctions_c.pdf" attr="" comment="" date="1432237677" name="corefunctions_c.pdf" path="corefunctions_c.pdf" size="4790654" stream="corefunctions_c.pdf" tmpFilename="/tmp/5ljjVbIew6" user="MartinTurner" version="1"

Revision 819 May 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 68 to 68
 

Contacts:

Changed:
<
<
Kris Tielemans: k.thielemans@ucl.ac.uk
>
>
Kris Thielemans: k.thielemans@ucl.ac.uk
  Ron Fowler: ronald.fowler@stfc.ac.uk
Line: 79 to 79
 
META FILEATTACHMENT attachment="05484183.pdf" attr="" comment="" date="1428482542" name="05484183.pdf" path="05484183.pdf" size="968059" stream="05484183.pdf" tmpFilename="/tmp/U5SvDC4XAI" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482639" name="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="624041" stream="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/IDfdQzbWQL" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482720" name="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="1151084" stream="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/cUyGCkjEXo" user="MartinTurner" version="1"
Added:
>
>
META FILEATTACHMENT attachment="CPP-logo2-DokChampa-cropped.png" attr="" comment="" date="1432051796" name="CPP-logo2-DokChampa-cropped.png" path="CPP-logo2-DokChampa-cropped.png" size="13758" stream="CPP-logo2-DokChampa-cropped.png" tmpFilename="/tmp/l0yPb8curL" user="RonFowler" version="1"

Revision 719 May 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 7 to 7
 This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020.

The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews‎ (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)‎

Added:
>
>

Mailing List

There is a JISCMAIL list at: https://www.jiscmail.ac.uk/CCP-PETMR

Easy to sign up by following this link.

 

Events

  • Initial kick-off meeting with the CoIs on the 1st of April at UCL

Revision 629 Apr 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.

Changed:
<
<
This new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
>
>
This new CCP PET/MR has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
  The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews‎ (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)‎

Events

  • Initial kick-off meeting with the CoIs on the 1st of April at UCL
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
Changed:
<
<
  • Initial meeting with the Working Group to be arranged for the end of April
>
>
  • Initial meeting with the Working Group has been arranged for the 13th May 2015 11:30 to 15:00 at St Thomas Hospital, London.
 

Reading Materials

Revision 508 Apr 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 22 to 22
 
Added:
>
>
MR References:

  • Jeffrey A. Fessler Model-Based Image Reconstruction for MRI 05484183.pdf
  • Image Reconstruction: An Overview for Clinicians Michael S. Hansen and Peter Kellman JOURNAL OF MAGNETIC RESONANCE IMAGING 41:573–585 (2015) Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf
  • Non-Cartesian Parallel Imaging Reconstruction Katherine L. Wright, Jesse I. Hamilton, Mark A. Griswold, Vikas Gulani and Nicole Seiberlich, PhD JOURNAL OF MAGNETIC RESONANCE IMAGING 40:1022–1040 (2014) Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf
  • MRI Temporal Acceleration Techniques Jeffrey Tsao and Sebastian Kozerke, JOURNAL OF MAGNETIC RESONANCE IMAGING 36:543–560 (2012)
 

Action List (from 1 April 2015)

Setup and access to web-site (potentially just IP address access to put some content on there), mailing lists etc.

Line: 61 to 68
 Martin Turner: martin.turner@stfc.ac.uk

-- MartinTurner - 10 Feb 2015

Added:
>
>
META FILEATTACHMENT attachment="05484183.pdf" attr="" comment="" date="1428482542" name="05484183.pdf" path="05484183.pdf" size="968059" stream="05484183.pdf" tmpFilename="/tmp/U5SvDC4XAI" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482639" name="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="624041" stream="Hansen_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/IDfdQzbWQL" user="MartinTurner" version="1"
META FILEATTACHMENT attachment="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" attr="" comment="" date="1428482720" name="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" path="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" size="1151084" stream="Wright_et_al-2014-Journal_of_Magnetic_Resonance_Imaging.pdf" tmpFilename="/tmp/cUyGCkjEXo" user="MartinTurner" version="1"

Revision 405 Apr 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

Line: 13 to 13
 
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
  • Initial meeting with the Working Group to be arranged for the end of April
Changed:
<
<
Contacts:
>
>

Reading Materials

PET References:

Action List (from 1 April 2015)

Setup and access to web-site (potentially just IP address access to put some content on there), mailing lists etc.

The PET reconstruction engine will initially be based on STIR, with git access available. Need to merge in a few local branches first (e.g. clean-up of GE contributed code) before open access.

For MR, we will this year (2015-2016) target the Gadgetron. http://gadgetron.github.io/ Experience and need to check out facilities etc.

For both, our intention is to create a user-friendly level "above" these such that at later stage we can add support for other packages. The super-level will need to have MATLAB support. It's still unclear if other target languages are desired. It could be that we create the "super-level" in C++, and then use SWIG to provide the MATLAB/Python/etc interface for instance.

Regarding SWIG. As I mentioned, "mainline" SWIG doesn't have any MATLAB support yet. This work was started by someone as a Google Summer of Code project in 2009 or so. It was then last year taken up by someone called Joel Andersson, and I helped taking it forward. It seems to have stalled a bit again. F ork from KT is on https://github.com/KrisThielemans/swig

"This is the one that at UCL we are currently using for creating MATLAB support for STIR. Joel's is on https://github.com/jaeandersson/swig he's a bit ahead of me now. He merged some things from master back in and made a few small updates. I expect that would work for us without trouble, but haven't tried yet (and there's no good test-suite yet). Joel's behind master again, but again I don't think that matters too much (because SWIG supports a lot of languages, there are a lot of updates that are irrelevant to the MATLAB side of things. The "core" itself of SWIG doesn't change a lot)."

"Brief summary of current status of MATLAB support in SWIG:

- a lot of things work. It works for STIR, and STIR is relatively complicated.

- there are some memory allocation problems such that at exit of MATLAB, or when clearing STIR variables/functions in MATLAB in the wrong order, MATLAB can crash (but I haven't seen a crash during normal usage anymore since quite a while).

- the SWIG test-suite for MATLAB is incomplete but does throw up some errors which will need fixing. A lot of these are on support for "directors" (to be able to extend C++ from in MATLAB), which is a "nice-to-have" feature, but not essential for us at this point.

- SWIG MATLAB Documentation is minimal right now

- the SWIG maintainers rightly insist on the test-suite to work, and having TRAVIS support. The latter is tricky as TRAVIS doesn't have MATLAB (no license). There has been some discussion on getting minimal "run swig + compile" support for this on TRAVIS (i.e. without running the tests in MATLAB).

I suggest that most "general" communications on SWIG happen via the SWIG-devel mailing list, as we don't want to solve this on our own. A relatively old post is for instance, http://swig.10945.n7.nabble.com/SWIG-for-MATLAB-An-update-and-call-for-collaboration-td13950.html "

I think we should use the STIR mailing lists for anything that applies to the general STIR audience. That way, we hopefully will get some help from the international community as well (and relief some of the pressure on me). STIR mailing list info is on the STIR website.

Contacts:

  Kris Tielemans: k.thielemans@ucl.ac.uk
Added:
>
>
Ron Fowler: ronald.fowler@stfc.ac.uk
 Martin Turner: martin.turner@stfc.ac.uk

-- MartinTurner - 10 Feb 2015

Revision 305 Mar 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
Changed:
<
<

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MP)

>
>

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MR)

  The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.
Changed:
<
<
This new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020. The PI is Kris Thielemans (UCL)
>
>
This new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020.

The PI is Kris Thielemans (UCL) and the CoIs are Julian Matthews‎ (UoManchester), Andrew Reader (KCL), Claudio Prieto Vasquez(KCL) and David Atkinson (UCL)‎

 

Events

Changed:
<
<
27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs? , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
>
>
  • Initial kick-off meeting with the CoIs on the 1st of April at UCL
  • 27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html
  • Initial meeting with the Working Group to be arranged for the end of April

Contacts:

Kris Tielemans: k.thielemans@ucl.ac.uk

 
Changed:
<
<
Contact Martin Turner: martin.turner@stfc.ac.uk
>
>
Martin Turner: martin.turner@stfc.ac.uk
  -- MartinTurner - 10 Feb 2015

Revision 205 Mar 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
Added:
>
>

Collaborative Computational Project in Positron Emission Tomography and Magnetic Resonance (CCP PET/MP)

 The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.
Changed:
<
<
This collaborative wiki is to initilise actions for the new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020.
>
>
This new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020. The PI is Kris Thielemans (UCL)

Events

27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs? , or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply). http://www.pet-mri.eu/PETMR_School_15.html

 
Changed:
<
<
Contact Martin Turner: martin.turner@stfc.ac.cuk
>
>
Contact Martin Turner: martin.turner@stfc.ac.uk
  -- MartinTurner - 10 Feb 2015 \ No newline at end of file

Revision 110 Feb 2015 - MartinTurner

Line: 1 to 1
Added:
>
>
META TOPICPARENT name="WebHome"
The UK has been at the forefront of many innovations in both positron emission tomography (PET) and magnetic resonance (MR) imaging, making the UK one of the world leaders in medical imaging since its inception. The recent integration of PET and MR into a single simultaneous imaging system opens up exciting potential for synergistic imaging, and this timely proposal of a collaborative computational project aims to bring together the best of the UK’s PET and MR image reconstruction expertise to capitalise on this unique opportunity.

This collaborative wiki is to initilise actions for the new CCP PET/MR that has been funded by the EPSRC from 1 April 2015 - 31 March 2020.

Contact Martin Turner: martin.turner@stfc.ac.cuk

-- MartinTurner - 10 Feb 2015

 
This site is powered by the TWiki collaboration platform Powered by Perl This site is powered by the TWiki collaboration platformCopyright & by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding TWiki? Send feedback