https://github.com/hbclab/uiowa-mri-course-2018

https://github.com/hbclab/uiowa-mri-course-2018

Repository

https://github.com/HBClab/uiowa-mri-course-2018/blob/master/

## Potential links/resources per topic
### **Introductions and overview**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0825_1_Neuroanatomy_introbasics.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0825_2_Hastings_Aguirre_2014.pdf : 2014 link

### **MRI physics**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0827_1_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch3_READp57-67.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0827_3_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch4_READp89-97.pdf : 2014 link
- https://practicalfmri.blogspot.com/2012/02/physics-for-understanding-fmri.html
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0827_2_CoxChap2.pdf : 2014 link
- https://www.youtube.com/watch?v=1CGzk-nV06g : 2014 link
- https://www.youtube.com/watch?v=djAxjtN_7VE&feature=youtu.be : 2014 link
- https://www.youtube.com/watch?v=7aRKAXD4dAg: 2014 link
- http://www.revisemri.com/tools/kspace/ : 2014 links
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0829_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch5.pdf : 2014 link
- http://www.revisemri.com/questions/kspace/ : 2014 link
- http://ctrl.ucla.edu/video/nitp/pages/07212014-ennis1 : 2014 **DEAD** link
- http://ctrl.ucla.edu/video/nitp/pages/07212014-ennis2 : 2014 **DEAD** link
- http://www.brainmapping.org/NITP/images/Summer2015Slides/Demos/K-SpaceDemos/KSpaceDemos.html : JK: another k space link
- http://events7.mediasite.com/Mediasite/Play/37504d321e43421893f8ce4b0a1719a81d?catalog=9fb9dc4c-d2bb-4f35-a172-6d8d804f3a66 : JK: long physics video
- http://www.med.harvard.edu/aanlib/basicsMR.html : 2014 HW#1 link
- https://fmrif.nimh.nih.gov/course/2017/05_Vinai_20170612 : JK: intro mri/physics

### **fMRI physics + BOLD contrast**
- https://fmrif.nimh.nih.gov/course/2017/08_Dan_20170619 : JK: what's neuronal vs. what's not
- http://events7.mediasite.com/Mediasite/Play/1ddbdd139f9e4cdcb8197d4c3656f5bc1d?catalog=9fb9dc4c-d2bb-4f35-a172-6d8d804f3a66 : JK: long physics video
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0903_1_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch6.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0903_2_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch7.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0905_Kwong-PNAS-1992.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0905_Ogawa-PNAS-1992.pdf : 2014 link
- https://www.youtube.com/watch?v=7mI4ieTPpmE : 2014 link

### **Getting started with Neurodebian: software and images**
- https://explainshell.com/ : JK: place to enter shell commands to explain them
- http://swcarpentry.github.io/shell-novice/ : JK: scripting practice
- https://www.youtube.com/watch?v=eqfjKV5XaTE : from neurodebian
- https://www.youtube.com/watch?v=-dPgYekeNEU&feature=youtu.be : 2014 from mwvoss

### **What are images and lab**
- http://dicomlookup.com/lookuppage.asp : JK: basic resource to look up dicom tags
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0908_Handbook_of_Functional_MRI_Data_Analysis_AppB.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0908_Handbook_of_Functional_MRI_Data_Analysis_AppC.pdf : 2014 link
- http://www.mccauslandcenter.sc.edu/crnl/tools/diy-fmri : 2014 **DEAD** link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0912_1_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch2.pdf : 2014 link
- https://brainder.org/2012/09/23/the-nifti-file-format/ : 2014 HW#1 link
- https://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hdr.html : 2014 HW#3 link
- http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer?focused=8628744&tab=function : 2014 HW#3 link
- https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dinfo.html : 2014 HW#3 link
- https://www.youtube.com/watch?v=IKDLEhetUsg : 2014 HW#3 link (explain 3dinfo)
- https://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q1 : JK: nifti faq
### **Image processing basics lab**
- http://nipy.org/nibabel/coordinate_systems.html : JK: understanding coordinates and affines
- https://github.com/poldrack/fmri-handbook-2e-code/blob/master/notebooks/Chapter2-ImageProcessing/Chapter2-ImageProcessing.ipynb : JK: poldrack notebook on similar subject
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0915_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch8.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0924_Handbook_of_Functional_MRI_Data_Analysis_2_Image_processing_basics.pdf : 2014 link
- https://www.youtube.com/watch?v=IxVxK12Z3Qo : 2014 HW#2 making masks mwvoss
- https://www.youtube.com/watch?v=D_TKXv8_IPQ : 2014 HW#3 link (toggle native space)
- https://www.youtube.com/watch?v=YI967Jbw_Ow : 2014 HW#4 link (x,y,z mri)
- http://www2.psychology.uiowa.edu/classes/31231/Labs/Lab4/PowerNeuroImage2012.pdf : 2014 HW#4 link (motion parameters)
- https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT : 2014 HW#5 link

### **Structural image quality**
- http://mriqc.readthedocs.io/en/latest/about.html : JK: mriqc structural qc

### **Structural segmentation and lab**
- https://www.youtube.com/watch?v=JPjJqUEhrTo : 2014 HW#5 link, editing brain masks

### **fMRI images: basics**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0924_Handbook_of_Functional_MRI_Data_Analysis_2_Image_processing_basics.pdf : 2014 link
- https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dmerge.html : 2014 HW#4 link
- https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg : 2014 HW#5 link

### **fMRI preprocessing: sources of noise**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0919_Handbook_of_Functional_MRI_Data_Analysis_Ch3.pdf : 2014 link
- https://en.wikibooks.org/wiki/Neuroimaging_Data_Processing/Temporal_Filtering : 2014 HW#4 link
- https://hubpages.com/education/Frequency-Hertz-and-Waves : 2014 HW#4 link
- http://mindhive.mit.edu/node/116 : 2014 HW#4 link
- http://mindhive.mit.edu/node/117 : 2014 HW#4 link
- http://mriqc.readthedocs.io/en/latest/about.html : JK: mriqc functional images
- https://fmrif.nimh.nih.gov/course/2017/07_Dan_20170619: JK: lecture about noise sources
### **fMRI preprocessing: smoothing**
- http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesSmoothing : 2014 HW#4 link
- http://andysbrainblog.blogspot.com/2012/06/smoothing-in-afni.html : 2014 HW#4 link
- https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBlurToFWHM.html : 2014 HW#4 link
- https://www.youtube.com/watch?v=wdw_-GQ0J_8 : 2014 HW#4 link

### **fMRI preprocessing: denoising and lab**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/0929_Kelly_JNeuroMethods_2009.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1001_McKeownHum%20Brain%20Mapp1998.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Lectures/DenoisingPractice/Example%20Denoising%20Procedure.pdf : 2014 link
- https://www.youtube.com/watch?v=fLuT6In4neE : 2014 HW#6 link melodic

### **Putting it all together for different designs**
- http://neuropowertools.org/ : JK: do a power analysis and/or design your experiment

### **Putting it all together with batch scripting and documenting your steps**

### **Statistical analysis: single subject task analysis**
- https://www.youtube.com/playlist?list=PLB2iAtgpI4YHlH4sno3i3CUjCofI38a-3 : JK: mumford FSL walkthrough
- http://www.brainvoyager.com/bvqx/doc/UsersGuide/StatisticalAnalysis/TheGeneralLinearModel.html : JK: explain GLM
- http://www.labkitty.com/2017/12/a-primer-on-general-linear-model.html : JK: explain GLM
- http://mindhive.mit.edu/node/55 : JK: explain single subject analsis concepts
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1013_Handbook_of_Functional_MRI_Data_Analysis_AppA.pdf : 2014 link explain GLM
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1013_Handbook_of_Functional_MRI_Data_Analysis_ch5.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1015_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch10.pdf : 2014 link
- https://www.youtube.com/watch?v=-LQomBKLa9w : 2014 HW#6 link glm gui mwvoss
- https://www.youtube.com/watch?v=UGTZ8CaScDQ : 2014 HW#8 feat model mwvoss
- https://www.youtube.com/watch?v=mgyAfunsV34 : 2014 HW#8 feat model andybrainblog pt. 1
- https://www.youtube.com/watch?v=TPR2v0mOxk8 : 2014 HW#8 feat model andybrainblog pt. 2
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1013_Handbook_of_Functional_MRI_Data_Analysis_ch5.pdf : 2014 HW#8 link
- https://www.youtube.com/watch?v=pAmQpJ52tfk : 2014 HW#8 feat model andybrainblog pt. 3
- https://www.youtube.com/watch?v=iX2otzlUSyk : 2014 feat output andybrainblog
- https://youtu.be/qkJwrYciraY : 2014 visualize feat results andybrainblog

### **Experimental design & project ideas**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1006_Functional%20Magnetic%20Resonance%20Imaging_Huettel_Ch9.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1008_AmaroBrain%20and%20Cognition2006.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/Schneider-GarcesJ%20Cogn%20Neurosci2010.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1010_MorcomNeuroImage2007.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1010_ChurchHum%20Brain%20Mapp2010.pdf : 2014 link
- https://mri.radiology.uiowa.edu/mediawiki/index.php/Optseq2help : 2014 link
- http://corticalexplorer.com/ : JK: learn brain anatomy
- http://neurosynth.org/ : JK: check out meta-analyses using peak coordinates
- https://neurovault.org/ : JK: check out meta-analyses using unthresholded maps
- http://brainmap.org/pubs/ : 2014 HW#7 link
- http://www2.psychology.uiowa.edu/classes/31231/Labs/Lab7/Eickhoff_ALE_methods_2012.pdf : 2014 HW#7 link
- http://brainmap.org/sleuth/ : 2014 HW#7 link
- https://brainmap.org/ale/ : 2014 HW#7 link
- http://brainmap.org/sleuth/manual.pdf : 2014 HW#7 link
- http://brainmap.org/scribe/ : 2014 HW#7 link
- https://youtu.be/i9R2Z_U8ucg : 2014 HW#8 test efficiency mwvoss
- https://youtu.be/rIa6_lPaqqM : 2014 HW#8 making timing files with pico

### **Between subjects analysis**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1020_Handbook_of_Functional_MRI_Data_Analysis_ch6.pdf : 2014 link
- http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesRandomFields : 2014 link
- https://www.youtube.com/watch?v=GL3qKdy6A-U : 2014 HW#9 group feat

### **Statistical inference on images**
- http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184923 : JK: statistical power paper
- http://mumfordbrainstats.tumblr.com/ : JK: general mumford tumbler
- http://www2.psychology.uiowa.edu/classes/31231/Readings/1022_Handbook_of_Functional_MRI_Data_Analysis_StatInference.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/Poldrack_reverse_inferenc_TICS_2006.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/BehrensTrends%20Cogn%20Sci%20(Regul%20Ed)2012.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/KriegeskorteNat%20Neurosci2009.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/KriegeskorteNatNeuro_supplmentary.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/Kriegeskorte_qa_2010.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Labs/Lab7/Fox_AnnReview_meta_analysis_2014.pdf : 2014 HW#7 link
- https://youtu.be/fIu4tUjRfUE : 2014 HW#10 making masks from atlas
- http://mumford.bol.ucla.edu/perchange_guide.pdf : 2014 HW#10 featquery mumford
- https://youtu.be/SNVt7smHLm8 : 2014 HW#10 featquery andybrainblog

### **Task analysis: putting it all together**

### **Introduction to Nipype and workflows**
- https://miykael.github.io/nipype_tutorial/ : JK: nipype tutorial


### **Resting state functional connectivty**
- http://www2.psychology.uiowa.edu/classes/31231/Readings/Cole_Frontiers_2008.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/O'ReillySocial%20Cognitive%20and%20Affective%20Neuroscience2012.pdf : 2014 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/SeeleyJ%20Neurosci2007.pdf : 2014 link
- https://youtu.be/rQtDQ-qYEpw : 2014 HW#11 group melodic
- http://www2.psychology.uiowa.edu/classes/31231/Readings/SmithProc%20Natl%20Acad%20Sci%20USA2009.pdf : 2014 HW#11 link
- http://www2.psychology.uiowa.edu/classes/31231/Readings/VincentNature2007.pdf : 2014 HW#13 link
- https://fmrif.nimh.nih.gov/course/2017/17_Catie_20170712 : JK: resting state lecture
- https://fmrif.nimh.nih.gov/course/2017/18_Gotts_20170714 : JK: another resting state lecture

### **Reporting your methods and results; final project working session**
- http://mvpa.blogspot.com/2013/04/caret-plot-nifti-image.html : 2014 caret
- https://www.youtube.com/playlist?list=PLylb26b_6ntNmw0RM3_ncJXaKwDVOu8VS : 2014 tim's playlist caret
- http://nilearn.github.io/plotting/index.html : JK: plotting with nilearn

### **Final project presentations**

### **Further Resources for asking questions**
- https://neurostars.org/
- https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=FSL
- https://afni.nimh.nih.gov/afni/community/board/list.php?1

### **OTHER**
- https://github.com/poldrack/fmri-analysis-vm/blob/master/analysis/introduction/Introduction%20to%20notebooks%2C%20plotting%2C%20nilearn%2C%20nibabel%20and%20nipype.ipynb : JK: intro to jupyter and other topics
- https://www.datacamp.com/community/tutorials/tutorial-jupyter-notebook : JK: jupyter notebook background

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