Getting started creating an entry

General steps

1. Edit and copy the syntax for the Template region entry to a new page in the WIKI under the appropriate heading. Change the region name. Click here for the Template

2. Identify the location of the structure

  • Do a search for fMRI studies of the structure name
  • For common structures, enter into Neurosynth.org and look for peak coordinate(s)

3. Find key papers

  Start with the {{:sample_endnote_library.enlp.zip|Template_Endnote_Library}} and do searches through Endnote (or Papers)
* For structures rarely activated specifically in fMRI studies, enter citations of papers activating/reporting coordinates under "Studies activating/Specifically named"
* In Neurosynth, enter coordinate(s) identified or average of coordinates, and find papers activating near the coordinate. Enter those under ""Studies activating/Coordinate based"

4. Add images, files, and other info from papers as you work (see below).

Notes: * Use the standard region names (e.g., “RVM”) in the first part of any file you upload/post to the WIKI. This will help keep it organized!

A specific idea: Step 1

These steps took me about 1 hour overall to generate the start of a new Region page. I followed them in order. Click here to go to the example page

Create new Endnote library with region name check “Save as Package”

…or start with this Template_Endnote_Library, and remove the papers

Rename Group Set (at left) as “Reviews” Groups in the Endnote Library Ctrl + click (Mac) and choose “Create Group Set” Create group sets for HUMAN, ANATOMY, and FUNCTION as well as REVIEWS Create groups under HUMAN: general_human (these will discuss the structure) Create groups under HUMAN: fMRI (these will specifically activate the structure) Etc.

Endnote: Find PDFs

Find fMRI/PET studies (this will work if there are only a few human studies!): Search Pubmed for “RVM” + “fMRI” Download all (if not too many) Drag relevant ones to fMRI group Click on fMRI group, highlight all references Go to References → Find Full Text (PDFs will be found and attached)

Locate region in humans (based on fMRI)

To get coordinates (for a rare area): Open the PDFs and copy the coordinates for the structure into a list.

Some papers may not actually activate the structure, and you can remove them (copy into ' or post them on a different region page.

Post coordinates on WIKI

For those that do have coordinates, if this is a rarely activated area, can be entered on the WIKI in a table entry (see the Template) e.g., Study Description x y z Kong 2010 RVM seed 4 -34 -50 Eippert 2009 Placebo > Control late pain 8 -38 -40 Eippert 2009 Placebo > Control early pain -6 -35 -39 Derbyshire 2009 Offset analgesia 18 -30 -30

Add image(s) of region from papers

You might screen-grab (I use Skitch) a representative image if it's really good and post on WIKI. the WIKI will take .pngs. It's really helpful to name the file something informative for upload. Also, make the figure a reasonable size using WIKI syntax. Click DocuWiki at the bottom of any WIKI page for syntax help. For example, adding ?75 after the image name in WIKI syntax resizes it to 75 pixels. e.g.: Kong et al. 2010

Create an add an image for a spherical ROI around key coordinate(s)

Once you have coordinates, you can create an ROI and visualize that, and post it on the WIKI: In Matlab, for example:

coord = [0 -36 -40];
cl = sphere_roi_tool_2008([], 6, coord);
save RVM_ROI_cl cl

You can compress (zip) and post the .mat file on the WIKI

Post the Endnote file to the WIKI

Post the Endnote file with attached (embedded) PDFs - Remove Unfiled references - Close library to save (empty trash = yes) - Post on WIKI

Last modified: 2017/05/13 02:15