fMRI Quality Analysis Pipelines

I have been working on a quality analysis of a set of fMRI data that I collected this year and I made a list of available sources from some websites, blogs, academical papers including set of codes and slides and wanted to share with anyone interested. I will be updating this page as I find any source along my analysis continues but here is the current list of the sources I have collected so far. I benefited from all, I hope they would work for you all too.

If you know any sources that you think they should be listed here please do feel free to add those here. You can either send me a pull request and reach me out through my email or twitter account.

Quality Analysis Sources

Web Pages

Harvard University's neuroimaging page gives detailed explanation of investigations you should run through your data. Although the page explains the pipeline through their system called CBSCentral, you still could learn quite bit details about quality analysis steps from this page.
Cambridge University's two webpage here and here gives you the indications of noise you might find in your data.
Cambridge University's wikipage on framewise displacement and functional connectivity
MIT's Mindhive has always been one of the websites I look for a help for fMRI data analysis and I highly recommend
I believe there is no need to promote, but a wonderful series of blog posts by practiCal fMRI could be found from here and here

Manuals

Massachussetts General Hospital's Quality Control Manual
University of Missouri's guideline
University of Newyork's fMRI Data Quality guideline
Ok, maybe this is not directly data quality book but I found it very useful and share with you guys from here now. I move it later when I open another page for tutorials etc., but please give credit to this work! Handbook of Structural Brain MRI Data Analysis by Jerome J Maller from Monash Alfred Psychiatry research center, Australia.

Presentations

MRI Quality Control Presentation by Natasha S. Hansen
CONN toolbox's quality assurance and analysis slides

Videos of MR Quality Assessments

Introduction to manual quality control in FSL by Harvard University.
Andrew Jahn's video on Quality Checks for fMRI Data

Workflows - Toolboxes

MRIQC by the Poldrack Lab at Stanford University
Cambridge University's data diagnostic webpage. This page explains how to extract mean and standart images from the data. I wrote the scripts in Matlab, the codes are available within my fMRI Quality Analysis Pipelines respository. Cambridge also provides a tsdiffana toolbox to plot the variations across the image-to-image and slice-to-slice intensity variance. I found those plots very useful to find out the noisy participants, I would strongly recommend you to use it as a starting QA analysis.
MIT's Artifact Detection toolbox ART
University of Pennsylvania QA Bash scripts to use on bold, dti and perfusion data
A blog post by CogNeuroStats on how to install use fBIRN QC/QA for data quality analysis
Standford's ArtRepair tool to check and repair the slice and volume artifacts in your data and gives a global summary across the subjects.
Rorden Lab's fMRI analysis and quality investigation scripts
NDS Lab's MRI preprocessing and quality analysis pipeline in which you could run a spike detection analysis, investigate the movement parameters you obtained in realignment, extract and plot mean image statistics across slices and images and plot the mosaic movies from your functional images. They also provide a preprocessing SPM batch scripts.
You can also find another set of scripts of Jeroen van Baar's Github page. The scripts contains function to detects spikes in the data and remove from it.
Codes from Parkes et al.'s paper listed below.
A toolbox by Stanford University for visual review and running semi-automatic detection and repair functions on fMRI data: ArtRepair