John Colby johncolby
johncolby
/ trk_plot.m.diff
Created
April 26, 2011 17:33
Tweak to trk_plot to highlight different levels
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/trk_plot.m b/trk_plot.m | |
| index 30e0a4a..26cf093 100644 | |
| --- a/trk_plot.m | |
| +++ b/trk_plot.m | |
| @@ -37,6 +37,9 @@ if nargin < 4 || isempty(slices), slices = header.dim/2; end | |
| if ~isstruct(tracks), error('Tracks must be in structure form. Try running TRK_RESTRUC first.'), end | |
| +levels = [0 25 50 75 100];^M | |
| +levels = round(levels*(97-1)/100 + 1);^M |
johncolby
/ between_grp.R.diff
Created
April 20, 2011 15:58
Modified to always do perms on all tracts/hemispheres
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/example/between_group/between_grp.R b/example/between_group/between_grp.R | |
| index ffeeaeb..e2d1c08 100644 | |
| --- a/example/between_group/between_grp.R | |
| +++ b/example/between_group/between_grp.R | |
| @@ -77,16 +77,7 @@ doPerms <- function(df, demog, nPerms=100){ | |
| maxT | |
| } | |
| -# Only correct for multiple comparisons across the tracts with a significant | |
| -# Point:Group interaction F-test. Set the corrected p-values of other tracts to 1 |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| exptDir = '/Users/jcolby/Documents/LONI/along-tract-stats/along-tract-stats.git/example/between_group' | |
| grpLabs = c('Control', 'FASD') | |
| thresh = 0.05 | |
| nPerms = 100 | |
| library(nlme) # Mixed-effects models | |
| library(ggplot2) # Plotting tools | |
| library(plyr) # Data manipulation | |
| library(RColorBrewer) # Color tables |
johncolby
/ trk_compile_data.patch
Created
March 29, 2011 17:08
Patches revision 72c87f6 of along-tract-stats to use normal structures instead of datasets
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| diff --git a/trk_compile_data.m b/trk_compile_data.m | |
| index 0b2ddfe..90d3d15 100644 | |
| --- a/trk_compile_data.m | |
| +++ b/trk_compile_data.m | |
| @@ -52,17 +52,12 @@ function [track_means,starting_pts_out] = trk_compile_data(subsDir,subIDs,tract_ | |
| if nargin < 7 || isempty(saveASCII), saveASCII = 0; end | |
| if nargin < 6 || isempty(saveTrk), saveTrk = 0; end | |
| if nargin < 5 || isempty(starting_pts_in) | |
| - starting_pts_in = dataset(); | |
| -elseif ~iscell(starting_pts_in.Subject) % Reformat to cells if subIDs are all numeric |
johncolby
/ my-first-style.xml
Created
February 4, 2011 23:59
Trying to add 'disambiguate-add-year-suffix' and 'collapse'
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" encoding="UTF-8"?> | |
| <style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" | |
| class="in-text"> | |
| <info> | |
| <title>My First Style</title> | |
| <id>my-first-style</id> | |
| <updated>2008-10-29T21:01:24+00:00</updated> | |
| </info> | |
| <macro name="author-short"> | |
| <names variable="author"> |
NewerOlder