@@ -6,7 +6,7 @@ This repository contains processing code and result files associated with the fo
### Lea Roumazeilles, Frederik J. Lange, R. Austin Benn, Jesper L. R. Andersson, Mads Frost Bertelsen, Paul R Manger, Edmund Flach, Alexandre A. Khrapitchev, Katherine L. Bryant, Jérôme Sallet, Rogier B. Mars
Explanations to use the scripts used for the results can be found in /scripts/scripts_README.md
Explanations to use the scripts used for the results can be found in scripts/Analysis and scripts/Template
Some scripts call other scripts from MrCat toolbox available at: https://github.com/neuroecology/MrCat
Raw data of the lemur and squirrel monkey will be made available on the Digital Brain Bank of the Wellcome Centre for Integrative Neuroimaging (https://open.win.ox.ac.uk/DigitalBrainBank/#/) upon acceptance of the paper. Macaque data are already available within PRIME-DE ((Milham et al. 2018); http://fcon_1000.projects.nitrc.org/indi/indiPRIME.html). The scripts used for preprocessing are available in MrCat (www.neuroecologylab.org, https://github.com/neuroecology/MrCat). MMORF is available as a Singularity image online (https://git.fmrib.ox.ac.uk/flange/mmorf_beta). The surface pipeline is available online (https://github.com/neurabenn/precon_all).
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@@ -16,7 +16,7 @@ Raw data of the lemur and squirrel monkey will be made available on the Digital
# Cortical morphology and white matter tractography of three phylogenetically distant primates: Evidence for a simian elaboration
Scripts in this repository will need preprocessed data output such as bedpostX folder and warp from subject space to standard space.
# Tractography
**1. Protocols**
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*)
(calls convert from imagemagick)
**2. Run xtract**
Files needed in tractography folder of each species: ```slist.txt``` file with all the tracts you want in format:
tract_l 10
tract_r 10
...
And ```options.txt``` with the options that you want to change from probtrackx
relevant scripts: ```wrapper_xtract.sh```
data needed: BedpostX data, wrap from standard to subject space and form subject to standard space
**3. Average the tracts across subject**
relevant scripts: ```average_tracts.sh```
Average tracts, log norm them and copy the results to the /average/all folder.
# Controls
**1. ILF parietal branch control**
protocols found in protocols folder with name 'test'
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*)
**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*)
data needed: bedpostX folder with nodif_brain_mask, standard images, warps from standard space to diffusion space and inversly and a surface midthickness for each species and a medial wall (named midline) mask.
This step creates a matrix defining the connectivity of each vertex to the GM to the rest of the brain.
**2. Average fdt_matrix2**
relevant scripts: ```average_fdt_matrix2.m```
This step average the matrices obtained at the previous stages across subjects.
**3. Create the surface tracts**
relevant scripts: ```create_surf_tract.m``` uses the multiply_fdt from MrCatDev
relevant files: in tractography/average and averaged matrices from previous step.
This step creates the surface tracts in a dtseries in tractography/average/surface/tract_surf.hemi.dtseries.nii
**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