Commit 1f351a40 authored by Lea Roumazeilles's avatar Lea Roumazeilles
Browse files

fix Readme

parent a5c9c106
......@@ -15,15 +15,21 @@ Raw data of the lemur and squirrel monkey will be made available on the Digital
Species could be: lemur, squirrel_monkey, macaque
Data are organised as follow:
Repositeory is organised organised as follow:
```
figures
|
+-- recipes (figures created with the scripts provided)
|
+-- templates (scene file to make figure 3)
+-- templates (scene file to make *figure 3*)
|
+-- tractography (scene file to make figure 5-8B)
+-- tractography (scene file to make figure *5-8B*)
scripts
|
+-- Analysis
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+-- scripts_README.md
species
|
......
......@@ -8,7 +8,7 @@ Each folder contains:
1 seed, 1 target, 1 exclude and 1 invert file.
ILF and MdLF test are for the control analysis.
relevant scripts to make the protocol figures: ```figure_tractography_recipes.sh``` (figure 1)
relevant scripts to make the protocol figures: ```figure_tractography_recipes.sh``` (*figure 1*)
(calls convert from imagemagick)
**2. Run xtract**
......@@ -35,16 +35,16 @@ Average tracts, log norm them and copy the results to the /average/all folder.
protocols found in protocols folder with name 'test'
relevant scripts: ```figure_tractography_recipes_ilfcontrol.sh``` to show the recipe figures (figure 2)
relevant scripts: ```figure_tractography_recipes_ilfcontrol.sh``` to show the recipe figures (*figure 2*)
Then ```wrapper_xtract.sh``` with a different slist to run the tractography for ilf_test and mdlf_test
Then ```figure_control_ilf.m``` to make the ratio and the figure. (uses individual data and boxplot_statistics.m script) (figure 6C)
Then ```figure_control_ilf.m``` to make the ratio and the figure. (uses individual data and boxplot_statistics.m script) (*figure 6C*)
**2. SLFc and OR control**
relevant scripts: ```figure_ratios_tracts.m``` (uses subplot_tight function) wich looks at ratio with according tracts (cbd or cbt) and then save figure (figure 8C)
relevant scripts: ```figure_ratios_tracts.m``` (uses subplot_tight function) wich looks at ratio with according tracts (cbd or cbt) and then save figure (*figure 8C*)
# Surface tracts
......@@ -74,16 +74,19 @@ This step creates the surface tracts in a dtseries in tractography/average/surfa
**4. Prepare the files to make a good workbench scenes**
Need to define a label list with the colors that you want (saved in script folder)
Ex:
```
CBd
1 255 94 87 255
Name
value of the tract in your dtseries / RGB code / alpha
```
relevant scripts: ```surf_tracts_smoothloglabel.sh``` (calls lognorm_surf_tract.m)
Then open the scene file: $WBDIR/wb_view figures/tractography/all_tracts_surface.scene and choose which tract (figures 5B, 6B, 7B, 8B)
Then open the scene file: $WBDIR/wb_view figures/tractography/all_tracts_surface.scene and choose which tract (*figures 5B, 6B, 7B, 8B*)
**5. Tracts and cortical labels**
In scene file all_tracts_surface.scene and open scene slfc_or_labels (figure 9).
In scene file all_tracts_surface.scene and open scene slfc_or_labels (*figure 9*).
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