Tuesday, July 31, 2012

(Medical) Imaging / PACS / DICOM / Health Informatics Conferences

Month-view of conference submission deadlines (on-going update)
HI HIC AMIA, HAC APAMI BHI
MI CARS MICCAI, MIUA CINC HAMLYN SPIE(MI), SIPAIM ISBI, RSNA ECR
CV ICIP ICCV ICPR, ECCV,
IPCV
BMVC, CAIP ACCV, SIBGRAPI ESR, ICPRAM CVPR
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

NEW JOURNAL ALERT:
Journal of Medical Imaging (SPIE) (http://spie.org/x102992.xml)




Journal  Field IF
JACC: Cardiovas Img MI 5.528
Circulation: Cardiovas Img MI 4.757
Med Img Analysis MI 3.681
IEEE T Med Img MI 3.799
J American Med Inf. Asso. MI 3.609
IEEE T Img Pro CV 3.111
Int J Cardiovas Img CV 2.539
Int J Med Inf HI 2.414
J of Dig Img MI/CV/HI 1.421
IEEE T Pattern Anal CV 4.908
Pattern Recogn CV 2.292
J Mach Learn Res CV 2.561
Ultrasound in Med & Bio MI/CV 2.455
Ann Biomed Eng MI/CV 2.575
IEEE T BIOMED ENG MI 2.575
COMPUTERIZED MEDICAL IMAGING AND GRAPHICS MI 1.664
Int J Cars MI MI 1.364
EUR J ECHOCARDIOGR MI 2.394
SIAM J Imaging Sci MI 2.867
EUR HEART J Cardiac Imaging MI 3.669



HI      Health Informatics
MI     Medical Images, Radiography, DICOM, PACS
CV    Computer Vision, Pattern Recognition, Machine Learning


TO DO:
- add more
- Attach links
- submission type
- other details


last updated (2014-10-07)

Wednesday, July 11, 2012

From Microsoft Word to Latex

As much as I want to work on my papers in Microsoft Word, its been proven minutes by minutes that working on an academic research paper is not feasible without the use of LaTex.  Here, in this article, from a 'noob's perspective, I will lay down some of the fundamentals that you will need in order to have  your latex environment setup, ready, runnin' & gunnin'.  Since i am writing a paper for an upcoming SPIE conference, i'll take SPIE style class as a reference. (http://kmh-lanl.hansonhub.com/spie/)


Assuming you have been working on papers using the followings:
1) Microsoft Word
2) Endnote

At the end of this article, you will be dropping the above two, and will then be using the followings extensively hereafter.
1) Miktex (Think of this as a Compiler/Interpreter)
2) TeXnicCenter (Think of this as an IDE)
3) JabRef (Think of this as a Reference Manager)



I) Download and Install


Download and Install the followings (All of the followings will be done with a 'default' installation) Note: The version numbers are as of writing.

  • Miktex 2.9 (http://miktex.org/2.9/setup)
  • TeXnicCenter 1 RC 1 Installer (http://www.texniccenter.org/resources/downloads/29)
  • JabRef 2.8.1 (http://jabref.sourceforge.net/)
Download from "HansonHub" (see above) and save them in a folder
  • spie.cls
  • spiebib.bst
  • ifthen.sty
  • cite.sty
  • article.tex
  • report.bib
  • mcr3b.eps

II) Setup Search Path for Miktex
  1. Start > All Programs > MikTex 2.9 > Maintenance > Settings > Roots [tab]
  2. Add the path, in my case, i added the path to "My Documents"\[Papers]\[Conference_Name]\[Year]\tex\latex\"
  3. Go back to General [tab]
  4. Click Refresh FNDB

III) Get TeXnicCenter going

When you first load TeXnicCenter, it will ask you for the root path to all your tex-related executables, in my case, i specified "C:\Program Files\miktex\miktex\bin".  It will then fill in the blanks for Yap and the rest.  

4) Start writing with the SPIE format

1) Open up article.tex (you can rename this to a more sensible filename)
2) Then, click on Project > Create with active file as main file
3) Press Ctrl F7, and then Press Ctrl F5, you shall see the LaTex with SPIE format 
(if you have any errors in the output window, post it up here as comments) You can also try refreshing FNDB, to see if some of the errors are resolved.

IV) EndNote to Bibtex

ENDNOTE first
  1. Open up Endnote
  2. Click on Edit > Output Styles > select "BibTex Export" or go to Style Manager, and enable "BibTex Export" Click Apply/OK
  3. While you are still in Endnote, select all your citations, Click on File > Export  > In the output style selection list, choose BibTex Export
  4. Give it a sensible file name (it has to be in .txt, you will need to rename to .bib as you as its done saving)
  5. Save it to the folder along with your article.tex in step 3

JabRef Now
  1. Open up JabRef
  2. Open the .bib file you created and renamed in the previous step
  3. It will prompt errors saying none of the citations has BibTex Key
  4. You will need to auto-generate, while you are in JabRef, press Ctrl-G, and you will see your BibtexKey columns being filled
  5. Save the .bib
V) Completing the Circle

  1. Go back to TeXnicCenter
  2. Scroll to the bottom where you should see \bibliography{report}
  3. Change it to the .bib you saved in the previous step but without .bib (at this step, i suggest you refresh FNDB, again)
  4. Press Ctrl F7, and then Press Ctrl F5, you shall see the LaTex with SPIE format (if you have any errors in the output window, post it up here as comments) You can also try refreshing FNDB, to see if some of the errors are resolved.   You might also want to try to give a testing citation or two, just add \cite{ONE_OF_YOUR_BIBTEX_KEY} in any of the paragraphs reasonably. 

This should be it !