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 yoursbatch_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 yoursbatch_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 theThe 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 usuallyvi
.- Press
i
to enter insertion mode and write your message - Press
ctrl-c
oresc
to exit insertion mode - Type
:wq
to save and quit or:q!
to quite without saving
- Press
-
The command
git status
will show files that have changed since the last commit. -
The command
git log
will show the commit history