Temporary tools to help with comparing decision tree modularized/unmodularized for tedana.
Instructions assume git repositories will be stored in ~/repositories
, and data will be stored in ~/tedana_testing
.
You will need to modify paths if your setup does not accomodate this.
Clone the tedana repository and add my fork as a remote (see here) via
# if this path does not exist, make it
mkdir ~/repositories
cd ~/repositories
git clone https://github.com/ME-ICA/tedana.git
cd tedana
git remote add jbteves https://github.com/jbteves/tedana.git
git fetch jbteves JT_DTM
Install it into your current environment (you may want a different one than the one you have activated!)
cd ~/repositories/tedana
pip install -e .
Get this tool by running
cd ~/repositories
git clone https://github.com/jbteves/dtm_tools.git
First, enter the repository for tedana.
cd ~/repositories/tedana
Change to a branch you'd like to test (most likely main) via
git checkout main
and then run tedana on a test data set, somewhere other than the repository, for example
cd ~/tedana_testing
and consider putting your data in a directory called test_data
, like this:
mkdir test_data
cp DATA_FILES test_data/
And then run main using a tedana call like this:
tedana \
-d DATA_FILES \
-e ECHO_TIMES \
--out-dir main_tedana_results
Then, re-enter the repository and change to the modularized branch via
cd ~/repositories/tedana
git checkout jbteves/JT_DTM
and then run tedana on a test data set.
Use the existing mixing matrix (main_tedana_results/desc-ICA_mixing.tsv
) with the --mix
option in order to guarantee the same ICA components and save time.
Use an output directory named dtm_tedana_results
.
The call should look something like
tedana \
-d DATA_FILES \
-e ECHO_TIMES \
--out-dir dtm_tedana_results \
--mix main_tedana_results/desc-ICA_mixing.tsv
After this completes, you can use the dtm tool via
python ~/repositories/dtm_tools/dtm_tool.py main_tedana_results/desc-tedana_metrics.tsv dtm_tedana_results/desc-tedana_metrics.tsv
For more options see
python ~/repositories/dtm_tools/dtm_tools.py -h
To run the kundu tree instead of the minimal tree, use the following call:
tedana \
-d DATA_FILES \
-e ECHO_TIMES \
--tree kundu \
--out-dir dtm_tedana_results \
--mix main_tedana_results/desc-ICA_mixing.tsv