Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove link to our private Google Drive subset of PredictHD dataset #666

Merged
merged 1 commit into from
Jul 10, 2024
Merged

Remove link to our private Google Drive subset of PredictHD dataset #666

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion miqa/learning/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,14 @@ pip install -r ./miqa/learning/requirements.txt
```

## Get the data
For example, copy [PredictHD_small](https://drive.google.com/drive/u/1/folders/1SYY5LdKvU6fHgty1ynYXsVzqhGamsZmM) from the shared Google Drive into `nn_work_dir`, as well as files `T1_fold0.csv`, `T1_fold1.csv` and `T1_fold2.csv` from [Learning](https://drive.google.com/drive/u/1/folders/1uT24WMjZLt7IJWPXR-K7YYwiFUSomr_L).
For example, copy `PredictHD_small` from the shared Google Drive into `nn_work_dir`, as well as files `T1_fold0.csv`, `T1_fold1.csv` and `T1_fold2.csv` from `Learning`.
Now edit the paths inside `T1_fold*.csv` files to match the path on your file system, e.g.:
```shell
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold0.csv
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold1.csv
sed -i 's+P:/PREDICTHD_BIDS_DEFACE/+/home/exampleUser/nn_work_dir/PredictHD_small/+g' T1_fold2.csv
```
Note: To access [PredictHD](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000222.v6.p2) data, a request needs to be made.
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@hjmjohnson is this the best contact information to leave here?


## Run training
To run training on the 3-fold cross-validation using fold 0 as validation set and folds 1 and 2 as training set, use:
Expand Down
Loading