HW7: First level analysis

Due 4/19.

Part 1: Finish in-class exercise

Complete the level 1 and level 2 analysis we started in class on 4/13. You do not need to submit anything, but you will need the level 2 outputs for all subjects for the 4/20 class meeting.

Part 2: Level 1 analysis on your data

Fork and clone this repository to the cluster. You will also want to clone the volume or surface repository that contains the processing scripts we discussed in class.
Edit contrasts.tsv to specify your first level contrasts of interests. These contrasts will compare different conditions within a single run of the task. If your analysis plan includes comparisons between different tasks/sessions/subjects, those will be calculated at the group level.
Edit sbatch_level1.sh to specify a level1 processing job for a specified subject/session/task/run.
Use the sbatch command to submit one run of your sbatch_level1.sh script and make sure it works.
Edit submit_level1.sh to use a loop to submit a level1 job for each run you need to analyze. You will need to pay careful attention to the paths in the script. This script will be run at the command line on the cluster, so the paths need to be specified with respect to the filesystem on the cluster, as opposed to a filesystem in a container.
Run your submit_level1.sh script to queue all the level 1 analyses.
Edit sbatch_level2.sh to specify a second level processing job that averages across runs. You can use this even if your data does not have multiple runs.
Once your level 1 analyses have completed, use the sbatch command to submit one run of your sbatch_level2.sh script and make sure it works.
Edit submit_level2.sh to use a loop to submit a level2 job for each subject/session/task you need to analyze. You will need to pay careful attention to the paths in the script. This script will be run at the command line on the cluster, so the paths need to be specified with respect to the filesystem on the cluster, as opposed to a filesystem in a container.
Run your submit_level2.sh script to queue all the level 2 analyses.

Submission

Use git to add, commit, push
Create a pull request

git workarounds

To associate your clone with your GitHub username, run the command
```
 git remote set-url origin \
 https://${USER}@github.uconn.edu/${USER}/hw7.git
```
in your hw7 directory. This will avoid the The requested URL returned error: 403 Forbidden while accessing error when pushing.
Use the command unset SSH_ASKPASS prior to pushing to avoid the error (gnome-ssh-askpass:19484): Gtk-WARNING **: cannot open display:
When committing, you can specify a short commit message on the command line with the -m option: git commit -m 'commit message'. If you do not do this, the default editor will open so you can write your commit message. The default is usually vi.
- Press i to enter insertion mode and write your message
- Press ctrl-c or esc to exit insertion mode
- Type :wq to save and quit or :q! to quite without saving
The command git status will show files that have changed since the last commit.
The command git log will show the commit history

ham19006/hw7

About

Resources

Stars

Watchers

Forks

Releases

Languages