minc toolkit extras LAVIS

Minc-Toolkit-Extras

This is a module that can be accessed in the ADA cluster from the LAVIS. The scripts are created and curated by Gabriel Devenyi from the CobraLab and you can check the list here: (https://github.com/CobraLab/minc-toolkit-extras).

We also have a fork of the toolkit in case we want to include more scripts.

Here I will add the explanation of each script:

create_civet_image_es.sh

To create effect sizes images from the Hedgen's G stat files from R. Here is an example of use. Run it first and check the maximum and minimum values to adjust the color map.

./create_civet_image_effectsize2.sh CIVET_2.0_icbm_avg_mid_sym_mc_left.obj lCT_group_mean_ES.csv -0.9,0.6 CIVET_2.0_icbm_avg_mid_sym_mc_right.obj rCT_group_mean_ES.csv -0.9,0.6 hedgesg-groupAD CT_group_wmCT_ES2.png