{"id":634,"date":"2022-10-26T17:22:21","date_gmt":"2022-10-26T17:22:21","guid":{"rendered":"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=634"},"modified":"2025-01-29T13:21:03","modified_gmt":"2025-01-29T13:21:03","slug":"fmri-learning-tracks","status":"publish","type":"page","link":"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=634","title":{"rendered":"How to learn fMRI? A guide to learning fMRI."},"content":{"rendered":"\n<p>We have two fMRI learning tracks; the fast track and the slow track. The fast fMRI track is useful for short term (1-2 months) interns and senior project students. For those who wish to get deeper into fMRI (Master&#8217;s &amp; PhD students, postdocs, long-term interns) should check the other track.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Fast-track fMRI<\/h2>\n\n\n\n<p>In this track, you will learn concepts such as:<\/p>\n\n\n\n<ul>\n<li>fMRI pre-processing on a basic scale<\/li>\n\n\n\n<li>General linear model<\/li>\n\n\n\n<li>Univariate analysis (beta values, contrasts, t-maps, f-maps and such)<\/li>\n\n\n\n<li>Basic fMRI experiment design<\/li>\n\n\n\n<li>Preparation of event\/onset files using MATLAB or Python<\/li>\n\n\n\n<li>SPM (Statistical Parametrical Mapping) toolbox<\/li>\n<\/ul>\n\n\n\n<p>That being said, here is a list of materials which can be covered within 10 days that will bring you to a position to do basic fMRI analysis:<\/p>\n\n\n\n<ul>\n<li>fMRI theory\n<ul>\n<li><a href=\"https:\/\/miykael.github.io\/nipype-beginner-s-guide\/neuroimaging.html#acquisition-of-mri-data\" target=\"_blank\" rel=\"noreferrer noopener\">Brief introduction to neuroimaging<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/playlist?list=PLyGKBDfnk-iDVpUGSR_GlDmQrZOS0Lk6k\" target=\"_blank\" rel=\"noreferrer noopener\">fMRI Bootcamp &#8211; MITCBMM<\/a> (watch the first 3 videos)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Univariate analysis\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n<ul>\n<li><a href=\"https:\/\/andysbrainbook.readthedocs.io\/en\/latest\/fMRI_Short_Course\/Statistics\/03_Stats_HRF_Overview.html\" target=\"_blank\" rel=\"noreferrer noopener\">HRF Overview<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.fmrib.ox.ac.uk\/primers\/appendices\/glm.pdf\" target=\"_blank\" rel=\"noopener\" title=\"\">Introduction to GLM<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/mriquestions.com\/general-linear-model.html\" target=\"_blank\" rel=\"noopener\" title=\"Additional GLM material\">Additional GLM material<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/andysbrainbook.readthedocs.io\/en\/latest\/SPM\/SPM_Short_Course\/SPM_05_1stLevelAnalysis.html\" target=\"_blank\" rel=\"noreferrer noopener\">SPM 1st level analysis<\/a> (only check the theoretical part, no need to check the application \/ code parts)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/playlist?list=PLGeuU8rOLt8x42DxZoZ3QIsVw6r9GCHjD\" target=\"_blank\" rel=\"noopener\" title=\"\">Pre-processing theory playlist by Monti UCLA<\/a><\/li>\n<\/ul>\n\n\n\n<ul>\n<li><a data-type=\"URL\" data-id=\"https:\/\/www.youtube.com\/watch?v=qnjiJ41cryQ&amp;list=PL0ka7t7wbhYhaZkuaNIMkDmd2LqK5IsOf&amp;index=2\" href=\"https:\/\/www.youtube.com\/watch?v=qnjiJ41cryQ&amp;list=PL0ka7t7wbhYhaZkuaNIMkDmd2LqK5IsOf&amp;index=2\" target=\"_blank\" rel=\"noreferrer noopener\">fMRI analysis playlist<\/a> (Particularly the GLM part to understand GLM better then watch the following deconvolution video)<\/li>\n<\/ul>\n\n\n\n<ul>\n<li><a href=\"https:\/\/andysbrainbook.readthedocs.io\/en\/latest\/FIR\/FIR_Overview.html\" target=\"_blank\" rel=\"noreferrer noopener\">FIR analysis<\/a><\/li>\n<\/ul>\n\n\n\n<ul>\n<li>Statistics\n<ul>\n<li><a href=\"https:\/\/www.tnu.ethz.ch\/fileadmin\/user_upload\/teaching\/Methods_Models2017\/05b_MultipleComparisonCorrection_4Web.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Correction methods for multiple comparisons\">Correction methods for multiple comparisons<\/a><\/li>\n\n\n\n<li>Correction methods videos\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=l3tZI8sBwrA&amp;pp=ygUgcmViZWNjYSBzYXggbXVsdGlwbGUgY29tcGFyaXNvbnM%3D\" target=\"_blank\" rel=\"noopener\" title=\"Rebecca Sax Multiple comparisons problem\">Rebecca Sax Multiple comparisons<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.coursera.org\/lecture\/functional-mri\/module-26-multiple-comparison-problem-in-fmri-3PUa6\" target=\"_blank\" rel=\"noopener\" title=\"Multiple comparisons problem\">Multiple comparisons problem<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.coursera.org\/lecture\/functional-mri\/module-27-fwer-correction-WhrBO\" target=\"_blank\" rel=\"noopener\" title=\"FWER correction\">FWER correction<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.coursera.org\/lecture\/functional-mri\/module-28-fdr-correction-NQcXh\" target=\"_blank\" rel=\"noopener\" title=\"FDR correction\">FDR correction<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.coursera.org\/lecture\/functional-mri\/module-29-pitfalls-and-multiple-comparisons-bco76\" target=\"_blank\" rel=\"noopener\" title=\"Pitfalls\">Pitfalls<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S0165027007004189?via%3Dihub\" target=\"_blank\" rel=\"noopener\" title=\"iTT correction article\">iTT correction article<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/web4.bilkent.edu.tr\/hcf\/wp-content\/uploads\/2022\/11\/lab_meeting_7.25.16.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Correction methods for fMRI\">Correction methods for fMRI<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=QEChkyri6-w\" target=\"_blank\" rel=\"noopener\" title=\"Hiding Vs. Highlighting fMRI Results\">Hiding Vs. Highlighting fMRI Results<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/RikHenson\/CognesticStats\" target=\"_blank\" rel=\"noopener\" title=\"Introduction to statistics for hypothesis testing\">Introduction to statistics for hypothesis testing<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<ul>\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/BasicOnsetFiles\" target=\"_blank\" rel=\"noopener\" title=\"vent\/onset files\">E<\/a><a href=\"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=960\" target=\"_blank\" rel=\"noopener\" title=\"vent\/onset files\">vent\/onset files<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>SPM 2nd level analysis\n<ul>\n<li><a href=\"https:\/\/www.fil.ion.ucl.ac.uk\/mfd_archive\/2007\/powerpoint%20presentations\/SPM%202nd%20level%20analysis.ppt\" target=\"_blank\" rel=\"noopener\" title=\"Second level analysis presentation\">Second level analysis presentation<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/emotion.utu.fi\/wp-content\/uploads\/2023\/09\/TUE_6_SS_2ND.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Second level analysis presentation\">Second level analysis presentation<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"http:\/\/andysbrainblog.blogspot.com\/2013\/10\/whats-in-spmmat-file.html\" target=\"_blank\" rel=\"noopener\" title=\"Contents of SPM.mat file\">Contents of SPM.mat file<\/a>\n<ul>\n<li><a href=\"https:\/\/www.jiscmail.ac.uk\/cgi-bin\/wa-jisc.exe?A2=ind1209&amp;L=SPM&amp;P=R28338&amp;K=2&amp;X=54A0569F96EA7D8296&amp;Y=tamergezici%40gmail.com\" target=\"_blank\" rel=\"noopener\" title=\"\">Alternative<\/a> to above<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Slow-track fMRI<\/h2>\n\n\n\n<p>This track covers all relevant features of fMRI including the physics, pre-processing steps, file and database formats, analysis methods, visualization of analysis results, fMRI experiment design efficiency.<\/p>\n\n\n\n<ul>\n<li><a href=\"https:\/\/miykael.github.io\/nipype-beginner-s-guide\/neuroimaging.html#acquisition-of-mri-data\" target=\"_blank\" rel=\"noreferrer noopener\">Brief introduction to neuroimaging<\/a><\/li>\n\n\n\n<li>fMRI Physics\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=-C84RFgyzuE\" title=\"\">What happens in the scanner during an fMRI scan?<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/youtu.be\/eN-zCoI_Ejc?t=119\" target=\"_blank\" rel=\"noopener\" title=\"fMRI physics (watch 02:00 to 17:00)\">fMRI physics (watch 02:00 to 17:00)<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=XsDXxgjEJVY\" target=\"_blank\" rel=\"noopener\" title=\"Princples of fMRI on Physics and MRI details\">Principles of fMRI on Physics and MRI details<\/a>  <\/li>\n\n\n\n<li><a href=\"\/\/www.fmrib.ox.ac.uk\/primers\/appendices\/mri_physics.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Brief introduction to fMRI physics\">Brief introduction to fMRI physics<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/nifti.nimh.nih.gov\/background\" target=\"_blank\" rel=\"noopener\" title=\"\">Introduction to NIfTI format<\/a><\/li>\n\n\n\n<li>BIDS format\n<ul>\n<li><a href=\"https:\/\/bids.neuroimaging.io\/index.html\" target=\"_blank\" rel=\"noopener\" title=\"About BIDS\">About BIDS<\/a> <\/li>\n\n\n\n<li><a href=\"https:\/\/bids-standard.github.io\/bids-starter-kit\/folders_and_files\/files.html\" target=\"_blank\" rel=\"noopener\" title=\"IDS filenames\">BIDS filenames<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/bids-standard.github.io\/bids-starter-kit\/folders_and_files\/folders.html\" target=\"_blank\" rel=\"noopener\" title=\"BIDS folders\">BIDS folders<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Preprocessing\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/playlist?list=PLGeuU8rOLt8x42DxZoZ3QIsVw6r9GCHjD\" target=\"_blank\" rel=\"noopener\" title=\"\">Preprocessing theory playlist by Monti UCLA<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/andysbrainbook.readthedocs.io\/en\/latest\/SPM\/SPM_Short_Course\/SPM_04_Preprocessing.html\" target=\"_blank\" rel=\"noopener\" title=\"SPM preprocessing steps\">Andy&#8217;s brain blog pre-processing<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/AnalysisPrinciples\" target=\"_blank\" rel=\"noopener\" title=\"CBU Analysis principles\">CBU Analysis principles<\/a> (read for additional exposure to the concepts)<\/li>\n\n\n\n<li><a href=\"https:\/\/web4.bilkent.edu.tr\/hcf\/wp-content\/uploads\/2022\/07\/Intro_fMRI_2010_01_preprocessing.pdf\" target=\"_blank\" rel=\"noopener\" title=\"CBU preprocessing primer\">CBU pre-processing primer<\/a> (read for additional exposure to the concepts)<\/li>\n\n\n\n<li><a href=\"https:\/\/crnl.readthedocs.io\/fieldmaps\/index.html\" target=\"_blank\" rel=\"noopener\" title=\"Fieldmaps\">Fieldmaps<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><strong>After completing the material up until this part, you can go to the &#8220;Fast-track fMRI&#8221; part and read the material there. Once you complete those sections, come back here and continue.<\/strong><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/playlist?list=PL20gKJcYxxBU3kXvu58vf-lL2XxtLHtRL\" target=\"_blank\" rel=\"noreferrer noopener\">Designing and Analysing fMRI Experiments &#8211; Joseph Devlin<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.fil.ion.ucl.ac.uk\/spm\/course\/slides22-may\/\" target=\"_blank\" rel=\"noopener\" title=\"Additional material (SPM course)\">Additional material (SPM course)<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.fil.ion.ucl.ac.uk\/spm\/course\/slides02\/overview\/Intro.htm\" target=\"_blank\" rel=\"noopener\" title=\"Karl Friston's fMRI notes\">Karl Friston&#8217;s fMRI notes<\/a><\/li>\n\n\n\n<li>MRIcroGL\n<ul>\n<li>MRIcroGL videos by Andrew Jahn\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=Htid2mbyav8\" target=\"_blank\" rel=\"noopener\" title=\"\">Part 1<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=eD87us76jN0\" target=\"_blank\" rel=\"noopener\" title=\"\">Part 3<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=8-pTS1Cc0RI\" target=\"_blank\" rel=\"noopener\" title=\"\">Part 4<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=CL9X3zPUYN0\" target=\"_blank\" rel=\"noopener\" title=\"\">MRIcroGL introduction<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/www.cgl.ucsf.edu\/home\/meng\/dicom\/mricrogl-manual.pdf\" target=\"_blank\" rel=\"noopener\" title=\"\">MRIcroGL manual<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"http:\/\/web4.bilkent.edu.tr\/hcf\/wp-content\/uploads\/2023\/02\/Basis-Functions.ppt\" target=\"_blank\" rel=\"noopener\" title=\"Basis functions\">Basis functions<\/a><\/li>\n\n\n\n<li>Parametric modulation\n<ul>\n<li><a href=\"https:\/\/andysbrainbook.readthedocs.io\/en\/latest\/PM\/PM_Overview.html\" target=\"_blank\" rel=\"noopener\" title=\"Introduction to parametric modulation\">Introduction to parametric modulation<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.bobspunt.com\/resources\/teaching\/single-subject-analysis\/parametric-modulation\/\" target=\"_blank\" rel=\"noopener\" title=\"Parametric Modulator demonstrated in MATLAB\">Parametric Modulator demonstrated in MATLAB<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=2W7Rso-4Hqg\" target=\"_blank\" rel=\"noopener\" title=\"\">Parametric Modulation video<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2535596\/\">Modelling with parametric modulators<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/ParametricModulations\" target=\"_blank\" rel=\"noopener\" title=\"Parametric modulator (CBU)\">Parametric modulator (CBU)<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>fMRI Design efficiency\n<ul>\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=avsYY5dbJ7g\" target=\"_blank\" rel=\"noopener\" title=\"fMRI paradigm design video 1\">fMRI paradigm design video 1<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=yQIgZJRlrcU\" target=\"_blank\" rel=\"noopener\" title=\"fMRI paradigm design video 2\">fMRI paradigm design video 2<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/DealingWithDifference\" target=\"_blank\" rel=\"noopener\" title=\"CBU Design efficiency tips\">CBU Design efficiency tips<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.fil.ion.ucl.ac.uk\/mfd_archive\/2017\/Schedule\/fMRI%20Design%20and%20Efficiency%20AH.pptx\" target=\"_blank\" rel=\"noopener\" title=\"UCL Design efficiency tips\">UCL Design efficiency tips<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.pallier.org\/lectures\/fmriefficiency.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Design efficiency tips by Christophe Pallier\">Design efficiency tips by Christophe Pallier<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/andysbrainblog.blogspot.com\/2012\/06\/design-efficiency.html\" target=\"_blank\" rel=\"noopener\" title=\"Design efficiency tips by Andrew Jahn\">Design efficiency tips by Andrew Jahn<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/afni.nimh.nih.gov\/pub\/dist\/HOWTO\/howto\/ht03_stim\/html\/stim_background.html\" target=\"_blank\" rel=\"noopener\" title=\"Design efficiency (AFNI)\">Design efficiency<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3277683\/\" target=\"_blank\" rel=\"noopener\" title=\"Event related fMRI\">Event related fMRI<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/doi.org\/10.1016\/S1053-8119(09)71198-X\" target=\"_blank\" rel=\"noopener\" title=\"Optimization of blocked designs in fMRI\">Optimization of blocked designs in fMRI<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1053811921010582\" target=\"_blank\" rel=\"noopener\" title=\"Hyperbolic trade-off of trial and sample sizes\">Hyperbolic trade-off of trial and sample sizes<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=jxiBSH1We68\" target=\"_blank\" rel=\"noopener\" title=\"fMRI pitfalls\">fMRI pitfalls<\/a><\/li>\n\n\n\n<li><a data-type=\"URL\" data-id=\"http:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/DataDiagnostics\" href=\"http:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/DataDiagnostics\" target=\"_blank\" rel=\"noreferrer noopener\">Data diagnostics<\/a><\/li>\n\n\n\n<li>Once the material above is completed, you will know univariate analysis. Then you can move onto more advanced analysis methods.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Advanced fMRI analysis methods<\/h2>\n\n\n\n<ul>\n<li>MVPA &#8211; Machine Learning classification\n<ul>\n<li><a data-type=\"URL\" data-id=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2014.00088\/full\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2014.00088\/full\" target=\"_blank\" rel=\"noreferrer noopener\">The Decoding Toolbox<\/a>\n<ul>\n<li><a href=\"https:\/\/fmrif.nimh.nih.gov\/course\/mvpa_course\/2017\/04_tutorial\" target=\"_blank\" rel=\"noopener\" title=\"TDT Video\">TDT Video<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/web4.bilkent.edu.tr\/hcf\/wp-content\/uploads\/2022\/08\/Intro_fMRI_2010_03_MVPA.pdf\" target=\"_blank\" rel=\"noopener\" title=\"Introduction to MVPA (CBU) \">Introduction to MVPA (CBU) <\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/fmrif.nimh.nih.gov\/public\/other-courses\/mvpa\" target=\"_blank\" rel=\"noopener\" title=\"MVPA course\">MVPA course<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ewi-psy.fu-berlin.de\/en\/psychologie\/einrichtungen\/ccnb\/content\/MVPA-Workshop\/Hebart.pdf\" target=\"_blank\" rel=\"noopener\" title=\"MVPA workshop\">MVPA workshop<\/a><\/li>\n\n\n\n<li>Joe Etzel <a href=\"https:\/\/mvpa.blogspot.com\/2015\/09\/how-to-do-cross-validation-have-to.html\" target=\"_blank\" rel=\"noopener\" title=\"Joe Etzel - Cross-validation\">Cross-validation<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4692520\/\" target=\"_blank\" rel=\"noopener\" title=\"LSA\/LSU\/LSS comparison\">LSA\/LSU\/LSS comparison<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>RSA &#8211; Representational Similarity Analysis\n<ul>\n<li><a data-type=\"URL\" data-id=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/neuro.06.004.2008\/full\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/neuro.06.004.2008\/full\" target=\"_blank\" rel=\"noreferrer noopener\">Representational similarity analysis \u2013 connecting the branches of systems neuroscience<\/a><\/li>\n\n\n\n<li><a data-type=\"URL\" data-id=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780128120286000276\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780128120286000276\" target=\"_blank\" rel=\"noreferrer noopener\">Representational Similarity Analyses: A&nbsp;Practical Guide for Functional MRI Applications<\/a> (accessible via Bilkent)<\/li>\n\n\n\n<li><a data-type=\"URL\" data-id=\"https:\/\/academic.oup.com\/scan\/article\/14\/11\/1243\/5693905\" href=\"https:\/\/academic.oup.com\/scan\/article\/14\/11\/1243\/5693905\" target=\"_blank\" rel=\"noreferrer noopener\">A Guide to Representational Similarity Analysis for Social Neuroscience<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1003553\" target=\"_blank\" rel=\"noreferrer noopener\">A toolbox for representational similarity analysis<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/mvpa.blogspot.com\/2014\/08\/more-on-ld-t.html\" target=\"_blank\" rel=\"noopener\" title=\"Linear discriminant t analysis (LD-t)\">Linear discriminant t analysis (LD-t)<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Data diagnostics<\/li>\n\n\n\n<li>PPI as GLM covariates<\/li>\n\n\n\n<li><a href=\"https:\/\/www.fmrib.ox.ac.uk\/primers\/appendices\/bayes.pdf\" target=\"_blank\" rel=\"noopener\" title=\"\">Bayesian inference for neuroimaging<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">MRI Physics &amp; acquisition<\/h2>\n\n\n\n<ul>\n<li>How MRI works:&nbsp;<a href=\"https:\/\/www.youtube.com\/playlist?list=PLkSVzqeK5v2C4X1G3IuRUQeNveNGNxZrn\" target=\"_blank\" rel=\"noopener\" title=\"How MRI works\">https:\/\/www.youtube.com\/playlist?list=PLkSVzqeK5v2C4X1G3IuRUQeNveNGNxZrn<\/a><\/li>\n\n\n\n<li>MR Physics:&nbsp;<a href=\"https:\/\/www.youtube.com\/playlist?list=PLBkfUPj1TSRqmh2pXV2t5bY5Qr3Z8AeOi\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.youtube.com\/playlist?list=PLBkfUPj1TSRqmh2pXV2t5bY5Qr3Z8AeOi<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=XgIytITAWe0&amp;list=PL0ka7t7wbhYhi30TPmaXe-IR91xyVTyg4\" target=\"_blank\" rel=\"noreferrer noopener\">MRI Pulse sequences playlist<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/youtu.be\/aK0FiHYIcU0\" target=\"_blank\" rel=\"noreferrer noopener\">Information regarding protocol parameters<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/www.mritoolbox.com\/Home.html\" target=\"_blank\" rel=\"noreferrer noopener\">MRI Toolbox (for selecting protocol parameters)<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/ImagingSequences\">MRC CBU Imaging Sequences<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/imaging.mrc-cbu.cam.ac.uk\/imaging\/TipsForDataAcquisition\" target=\"_blank\" rel=\"noreferrer noopener\">Tips for data acquisition<\/a><\/li>\n\n\n\n<li>Understanding fMRI artifacts:&nbsp;<a href=\"https:\/\/practicalfmri.blogspot.com\/2011\/11\/understanding-fmri-artifacts.html\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/practicalfmri.blogspot.com\/2011\/11\/understanding-fmri-atifacts.html<\/a><\/li>\n\n\n\n<li>How to understand good data:&nbsp;<a href=\"https:\/\/practicalfmri.blogspot.com\/2011\/11\/understanding-fmri-artifacts-good.html\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/practicalfmri.blogspot.com\/2011\/11\/understanding-fmri-artifacts-good.html<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/watch?v=xpHzkg4JOkU\" target=\"_blank\" rel=\"noreferrer noopener\">Setting your experiment not for success, but less failure<\/a><\/li>\n\n\n\n<li>Harvard fMRI physics and protocol Q&amp;A:&nbsp;<a href=\"https:\/\/cbs.fas.harvard.edu\/science\/core-facilities\/neuroimaging\/information-investigators\/MRphysicsfaq\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/cbs.fas.harvard.edu\/science\/core-facilities\/neuroimaging\/information-investigators\/MRphysicsfaq<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/web4.bilkent.edu.tr\/hcf\/wp-content\/uploads\/2022\/07\/3T_user_training_FAQ_08Mar2012.doc\">3T User Training FAQ (by UC Berkeley Dr. Ben Inglis): Download<\/a><\/li>\n<\/ul>\n\n\n\n<p>Extras<\/p>\n\n\n\n<p><a href=\"https:\/\/en.wikibooks.org\/wiki\/SPM\" target=\"_blank\" rel=\"noopener\" title=\"SPM Wikibook\">SPM Wikibook<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>We have two fMRI learning tracks; the fast track and the slow track. The fast fMRI track is useful for short term (1-2 months) interns and senior project students. For those who wish to get deeper into fMRI (Master&#8217;s &amp; PhD students, postdocs, long-term interns) should check the other track. Fast-track fMRI In this track, &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=634\" class=\"more-link\">Read the full post &rarr;<span class=\"screen-reader-text\">&#8220;How to learn fMRI? A guide to learning fMRI.&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"om_disable_all_campaigns":false,"_mi_skip_tracking":false},"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/634"}],"collection":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=634"}],"version-history":[{"count":151,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/634\/revisions"}],"predecessor-version":[{"id":1323,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/634\/revisions\/1323"}],"wp:attachment":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=634"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}