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Module 9 Resting State fMRI with CONN
CONN is a front-end for SPM, which is one of the most influential fMRI software packages.
Spend time on the CONN website: https://web.conn-toolbox.org/
Watch the CONN tutorials from the development team: https://web.conn-toolbox.org/tutorials
Here's a brief manual for CONN that's worth being aware of if you have any questions but reviewing it isn't necessary for the homework: https://web.conn-toolbox.org/resources/manual
Here is the full manual for the software for additional information (useful if you use CONN for research): https://ufl.instructure.com/courses/499417/files/86163498?wrap=1
Other tutorials are available here if you need them (much better than mine but not specific to the homework). If you get stuck, I strongly recommend going through these: https://andysbrainbook.readthedocs.io/en/latest/FunctionalConnectivity/CONN_Overview.html
When you are done with this, move on to the next step.
This video will walk you through preprocessing data and running an analysis. This assignment will take multiple hours to finish, although you do not need to be at the computer for much of that!
This video is not pre-scripted. It's somewhat of a stream of consciousness approach. Note that I do go back and remove 4 participants who have low quality scans. You do not have to remove them, but I recommend you do. This will allow you to have more valid data.
https://youtu.be/4NBcK4CqKzs?si=k1nm-BOJYsQgOdi1
There are other analyses you can do. I encourage you to figure out one additional analysis I did not demonstrate.
After going through the video, you should be done with the homework, other than taking a screenshot of some results! Again, I recommend you try doing a different analysis. This will require creating a different 2nd-level covariate.
If you get stuck, I strongly recommend going through these tutorials. They are not specific to our homework data, but they will help you troubleshoot: https://andysbrainbook.readthedocs.io/en/latest/FunctionalConnectivity/CONN_Overview.html
If you are missing the HPC Slurm profile in CONN follow these instructions to add one: https://youtu.be/JREsfLO3ukI
When you add this, check the box to make it the default profile.
Here is what goes in the profile (also in the YouTube video description):
#Profile name
HPC Slurm
#Command used to submit a job
sbatch --job-name=JOBLABEL --error=STDERR --output=STDOUT OPTS SCRIPT
#Command used to delete a submitted job (optional)
scancel JOBID
#Command used to check the status of a submitted job (optional)
squeue --jobs=JOBID
#Additional submit settings (optional)
#in-file
#SBATCH --time=20:00:00
#SBATCH --mem=8gb
#SBATCH --account=clp7934
#SBATCH --qos=clp7934-b
Make sure Check job status automatically is checked
The videos below are from past years and can be referenced for more discussion but do not have to be viewed because much of the information is covered above.
#1: This video covers displaying ROI-to-ROI results.
#2 (watch the first part of option 1 video to see setting up covariates): Displaying seed/ROI to voxel.
Running CONN on HiPerGator: https://youtu.be/nTsJfkzxxT4
Here is a video walking you through running simple 2nd level analyses and displaying the results (from past years): https://youtu.be/iI9UZoyn318
Using a set of provided subjects with fMRI data, process the data through and including the 2nd level analysis stage using CONN. Covariates will be provided for you to input. This homework is due at the end of the weeks covering CONN.
A screenshot of a second-level analysis. You do not need to have any covariates, although I recommend you have at least one. You can submit a picture of either a seed to voxel (shown in the video) or ROI to ROI connection (shown with a different dataset in a different video listed on the module page).