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creating_getting_started [2012/06/29 00:02]
127.0.0.1 external edit
creating_getting_started [2017/09/27 22:54]
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-====== Getting started creating an entry ====== 
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-==== General steps ==== 
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-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. 
-[[template|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! 
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-==== 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. 
-[[rvm|Click here to go to the example page]] 
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-=== Endnote Search === 
- 
-Create new Endnote library with region name 
-check "Save as Package"​ 
- 
-...or start with this {{:​sample_endnote_library.enlp.zip|Template_Endnote_Library}},​ and remove the papers 
- 
-Rename Group Set (at left) as "​Reviews"​ 
-{{ :​sample_endnote_groups.png|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. 
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-== 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) 
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-=== 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. 
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-== 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 
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-== 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-2010-intrinsic_functional.pdf.png?​200|Kong et al. 2010}} 
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-== 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: 
-<code matlab> 
-coord = [0 -36 -40]; 
-cl = sphere_roi_tool_2008([],​ 6, coord); 
-save RVM_ROI_cl cl 
-</​code>​ 
- 
-You can compress (zip) and post the .mat file on the WIKI 
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-=== 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 
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