Describe NeuroanatomyTutorial here.


<h2><span>Jessica's neuroanatomy tutorial for imagers (MRC CBU skills seminar)</span></h2>

(compiled by Jessica Grahn, largely from the web)<br />
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<img width="449" height="339" alt="brain lobes" src="/people/jessica.grahn/brain_lobes.gif" /><br />
If only the brain really did come in colours...<br />
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Here are the important <span>orientation words</span> for describing brain positions:<br />
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<div><em>Coronal</em><span>:</span> Sections looking head-on toward an upright subject directly facing you <em><br />
Sagittal</em><span>:</span> Sections looking head-on toward an upright subject facing sideways <em><br />
Horizontal</em><span>:</span> Also known as transverse or axial sections, are parallel to the floor when the subject is standing upright</div>
<div><img width="224" vspace="5" hspace="20" height="185" class="middle" alt="planes" src="/people/jessica.grahn/neuroanatomyfiles/planes.GIF" /></div>
<div><strong><span>anterior</span></strong> (towards the front) <strong><span>posterior</span></strong> (towards the rear)<br />
<strong><span>superior</span></strong> ("above") <strong><span>inferior</span></strong> ("below")<br />
<strong><span>medial</span></strong> (towards the midline) <strong><span>lateral</span></strong> (away from the midline)<br />
<strong><span>rostral</span></strong> (towards the nose; Lat. rostrum, beak) <strong><span>caudal</span></strong> (towards the tail; Lat. cauda, tail)<br />
<strong><span>dorsal</span></strong> (towards the back; Lat. dorsum, back) <strong><span>ventral</span></strong> (towards the belly; Lat. venter, back)</div>
<div><img vspace="5" hspace="20" alt="Orientation.gif" src="/people/jessica.grahn/neuroanatomyfiles/Orientation.gif" /></div>
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<p><strong><span>The AC/PC line</span></strong></p>
<p><img width="600" height="1243" src="/people/jessica.grahn/neuroanatomyfiles/ACPCline.png" alt="acpcline" /></p>
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<p><strong><span>The cerebellum</span></strong><br />
(Schmahmann, J.D., <em>et al.</em>, Neuroimage, 1999, 10:233-260. )<br />
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<img class="c10" alt="gamma_sagslice.gif" src="/people/jessica.grahn/neuroanatomyfiles/gamma_sagslice.gif" /><br />
<img width="600" height="400" class="c11 c1 c2" alt="cerebellum_gammasurf_lobes.gif" src="/people/jessica.grahn/neuroanatomyfiles/cerebellum_gammasurf_lobes.gif" /></p>
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<strong><span>The basal ganglia.</span></strong><br />
Caudate, putamen, globus pallidus (called pallidum by AAL template).<br />
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<img width="600" height="684" alt="BG.png" src="/people/jessica.grahn/neuroanatomyfiles/BG.png" class="c12" /><img width="600" height="659" class="c13" src="/people/jessica.grahn/neuroanatomyfiles/BG_nooutline.png" alt="BG_nooutline.png" /><br />
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<p><strong>The caudate, putamen, and ventral striatum (the most ventral outline).</strong></p>
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<img width="700" height="279" class="c14" alt="Nature_ventral_striatum.jpg" src="/people/jessica.grahn/neuroanatomyfiles/Nature_ventral_striatum.jpg" /></p>
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<strong><span>The thalamus</span></strong><br />
<img width="600" height="601" class="c15" alt="Thalamus.png" src="/people/jessica.grahn/neuroanatomyfiles/Thalamus.png" /><br />
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<strong><span>The colliculi (superior colliculus and inferior colliculus).</span></strong><br />
In the z direction, once you see the colliculi, you are not in the thalamus anymore)<br />
The upper left picture has crosshairs on the superior colliculus, the rest are centred on the inferior colliculus.<br />
<img width="600" height="498" class="c16" alt="colliculi.png" src="/people/jessica.grahn/neuroanatomyfiles/colliculi.png" /><br />
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<p><strong>In cortex,</strong> <a href="http://en.wikipedia.org/wiki/Brodmann_area" target="_blank"><strong>Brodmann areas</strong></a> <strong>are often used in conjunction with anatomical lables to help specify an area.</strong></p>
<p>Brodmann areas: some common associated functions.<br />
1, 2, 3 = primary sensory cortex<br />
4 = motor cortex<br />
5, 7 = secondary sensory cortex<br />
6 = supplementary motor area (medial) and premotor cortex (lateral)<br />
8 = frontal eye fields<br />
9/46 = dorsolateral prefrontal cortex<br />
10 = frontopolar cortex<br />
11, 12 = orbitofrontal areas<br />
17 = primary visual cortex<br />
18, 19, 20, 21, 37 = secondary visual cortex<br />
24, 32 = anterior cingulate cortex<br />
41 = primary auditory cortex<br />
22, 42 = secondary auditory cortex<br />
39 = angular gyrus, part of Wernicke's area<br />
40 = supramarginal gyrus, part of Wernicke's area<br />
44/45 = Broca's Area<br />
47 Ventrolateral prefrontal cortex<br />
(13, 14, 15, 16, 27, 49, 50, 51 - monkey only)<br class="c18" />
Brodmann area 48 was described by Brodmann, but does not appear in his maps.<br />
<img class="c19" alt="brainbrodmannareas.gif" src="/people/jessica.grahn/neuroanatomyfiles/brainbrodmannareas.gif" /></p>
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<strong><span>The Medial Temporal Lobe (hippocampus/parahippocampal gyrus/amygdala/fusiform gyrus).</span></strong><br />
(Parahippocampal gyrus roughly intersects with Brodmann areas 27, 28, 34, 35, 36)<br />
(Fusiform gyrus contains part of Brodmann area 37)<br />
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<img width="600" height="617" alt="HC.png" src="/people/jessica.grahn/neuroanatomyfiles/HC.png" class="c20" /><img width="600" height="645" class="c23" alt="HCPHCFGamyg2.png" src="/people/jessica.grahn/neuroanatomyfiles/HCPHCFGamyg2.png" /><br />
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<strong><span>The lateral temporal lobe (ITG, MTG, STG, HG, and temporal poles).</span></strong><br />
Heschl's gyrus also called transverse temporal gyrus, with STG it contains primary auditory cortex, Brodmann areas 41 and 42.<br />
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<img width="600" height="681" class="c24" alt="LateralTemporal1.png" src="/people/jessica.grahn/neuroanatomyfiles/LateralTemporal1.png" /><br />
<img width="600" height="678" class="c25" alt="LateralTemporal2.png" src="/people/jessica.grahn/neuroanatomyfiles/LateralTemporal2.png" /><br />
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<p><strong><span>The pre-supplementary motor area/sma: medial Brodmann area 6</span></strong></p>
<p>y = 0 is considered by most to be the dividing line between the pre-SMA and the SMA.<br />
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<img width="600" height="647" class="c26" src="/people/jessica.grahn/neuroanatomyfiles/SMApre-SMA.png" alt="SMApre-SMA.png" /></p>
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<p><strong><span>The</span> premotor cortex</strong></p>
<p><span>in blue. Also Brodmann area 6, but lateral to the</span> SMA <span>(red).</span></p>
<table width="400" cellspacing="1" cellpadding="1" border="1">
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<p><img width="159" height="178" src="/people/jessica.grahn/neuroanatomyfiles/PMCSMA_axial.png" alt="pmcsmaaxial" /></p>
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		<td><img width="180" height="160" src="/people/jessica.grahn/neuroanatomyfiles/PMCSMA_coronal.png" alt="PMCSMAcoronal" /></td>
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<strong><span>The anterior cingulate.</span></strong><br />
Generally taken to have <em>cognitive</em> (red) and <em>affective</em> (blue) divisions. Brodmann areas 24 and 32.<br />
For excellent review (from which this figure was taken, click <a href="http://download.cell.com/trends/cognitive-sciences/pdf/PIIS1364661304002657.pdf" target="_blank">here</a>)<img width="477" height="423" src="/people/jessica.grahn/neuroanatomyfiles/cingulate.PNG" alt="cingulate" /><br />
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<p><strong><span>The frontal lobe.</span></strong><br />
The superior (red), middle (blue), and medial (green on midline) frontal gyri.<br />
The inferior frontal gyrus (par opercularis (pink), pars triangularis (green), pars orbitalis (yellow)).</p>
<table width="500" cellspacing="1" cellpadding="1" border="1">
	<tbody>
	<tr>
		<td><img width="217" height="217" src="/people/jessica.grahn/neuroanatomyfiles/frontal_lobe.png" alt="frontal1" /></td>
		<td><img width="217" height="217" src="/people/jessica.grahn/neuroanatomyfiles/frontal_lobe_Rwhite.png" alt="frontal2" /></td>
	</tr>
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</table>
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<strong>The inferior frontal gyrus</strong></p>
<p>Divisions of the IFG roughly correspond to BA 44, BA 45, and BA 47 (44/45 = Broca's area, 47 = VLPFC)</p>
<p>Brodmann areas 9/46 = DLPFC, Brodmann area 47 = VLPFC</p>
<p><img width="467" height="329" src="/people/jessica.grahn/neuroanatomyfiles/brainbrodmannareas_2.GIF" alt="brodmann areas 2" /></p>
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<p><strong><span>The parietal lobe.</span></strong><br />
Brodmann areas 5 (green) and 7 (yellow) = superior parietal lobule<br />
Brodmann areas 39 (red) and 40 (blue) = inferior parietal lobule<br />
Brodmann area 39 = angular gyrus, Brodmann area 40 = supramarginal gyrus</p>
<table width="500" cellspacing="1" cellpadding="1" border="1">
	<tbody>
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		<td><img class="c48" alt="parietal_rend_posterior" src="/people/jessica.grahn/neuroanatomyfiles/parietal_rend_posterior.png" /></td>
		<td><img width="177" height="170" src="/people/jessica.grahn/neuroanatomyfiles/parietal_rend_posterior45.png" alt="parietal 45 degree angle" /></td>
		<td><img width="185" height="159" src="/people/jessica.grahn/neuroanatomyfiles/parietal_rend_posterior90.png" alt="parietal 90 degress" /></td>
	</tr>
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</table>
<p>Intraparietal sulcus divides superior and inferior lobules (yellow line on picture below)</p>
<p><img width="421" height="484" src="/people/jessica.grahn/neuroanatomyfiles/intraparietal_axial.jpg" alt="ips" /></p>
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<p><strong><span>The occipital lobe</span></strong><br />
Brodmann areas 17 (primary visual cortex, blue), 18 and 19 (red and green, secondary visual cortex).<br />
<img class="c52" alt="occipital_rend_posterior.png" src="/people/jessica.grahn/neuroanatomyfiles/occipital_rend_posterior.png" /></p>
<p><br class="c54" />
<span>Structural and functional anatomy related to the visual system: a nice picture (from American Scientist magazine).</span><br />
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<a href="http://www.condition.org/relation.htm" target="_blank"><img class="c56" alt="vis system pic" src="/people/jessica.grahn/neuroanatomyfiles/clip_image001.jpg" />vis</a></p>
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<p><strong><span>Links.</span></strong></p>
<p>A very comprehensive <a href="http://www.radnet.ucla.edu/sections/DINR/index.htm" target="_blank">neuroanatomy site covering the entire brain: neuroimaging/vasculature/syndromes/pathology and quizzes.</a></p>
<p>This is an excellent site with MRIs, cadaver brains, and animations of brain structures (and you can quiz yourself!).<br />
<a href="http://www9.biostr.washington.edu/da.html" target="_blank">http://www9.biostr.washington.edu/da.html</a><br />
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The <a href="http://psychology.uwo.ca/fmri4newbies" target="_blank">fMRI for Newbies site</a> is filled with excellent information, including <a href="http://psychology.uwo.ca/fmri4newbies/BrainAnatomy.html" target="_blank">a page on functional anatomy</a>.</p>
<p>Clickable MRI and modelled brain sections yoked together. Click on Brain or detailed Brain.<br />
(once you've loaded the brain, read the buttons at the top and experiment a bit to see how they work: 'remove model' and 'cross-reference' are handy places to start.<br />
<a href="http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/AnatomyBrowser/current/models/brain/java/brain.html" target="_blank">http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/AnatomyBrowser/current/models/brain/java/brain.html</a><br />
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Site with clickable list of neuroanatomical terms, with pictures.<br />
<a href="http://www.sylvius.com/" target="_blank">http://www.sylvius.com/</a><br />
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If you're desperate to know about sulci, this manual with pictures may be helpful.<br />
<a class="moz-txt-link-freetext" target="_blank" href="http://www.cma.mgh.harvard.edu/manuals/parcellation/">http://www.cma.mgh.harvard.edu/manuals/parcellation/</a><br />
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A less comprehensive (and more comprehensible) sulci description can be found here:<br />
<a href="http://psychology.uwo.ca/fmri4newbies/PrimeronCorticalSulci.html" target="_blank">http://psychology.uwo.ca/fmri4newbies/PrimeronCorticalSulci.html</a><br />
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<strong>Software</strong><br />
I use <a href="www.mricro.com" target="_blank">MRIcro</a>, <a href="http://www.sph.sc.edu/comd/rorden/mribeta.zip" target="_blank">MRIcrobeta</a>, and <a href="http://www.sph.sc.edu/comd/rorden/mricron/" target="_blank">MRIcron</a> on Windows, and the <a href="http://www.fz-juelich.de/inb/inb-3/spm_anatomy_toolbox" target="_blank">Anatomy</a> toolbox in SPM (installed locally).</p>
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MRIcro beta version, a selection of the handy features (from Chris Rorden):<br />
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<div class="c59"><small class="c60">1.</small> <small class="c60">BatchConvertROIsToAnalyze: Convert numerous ROIs to Analyze format.</small><small class="c60"><br />
2. Convert NIfTI hdr/img to nii: combines the information of a hdr and img file into a single nii file.<br />
3. ResliceImage: convert anisotropic image to isotropic (e.g. 1x1x2mm -&gt; 1x1x1mm). (SPM's spline based reslicing is better, though)<br />
4. unNIfTI header: Turn a NIfTI hdr/img pair into a Analyze hdr/img pair that you can read with SPM2. It eliminates the NIfTI affine transformation matrix, so backup headers if you still hope to use SPM5<br />
5. Interpolate ROI slices - allows a user to only draw an ROI on a few slices and then interpolate missing slices.<br />
6. RescaleImageBy0.001: Useful for FSL's FUGUE tool when phase-unwrapping Philips images.<br />
7. IntensityNormalization: A simple global scaling function.<br />
8. ZeroImage: allows you to remove edges of image to aid brainextraction.</small> <small class="c60">(more sophisticated version is in MRIcron: Crop Edges)</small><small class="c60"><br />
9. Derivative: Takes a 4D image and makes a new 4D image where each volume shows the difference in signal relative to the previous volume.<br />
10.</small> <small>peristimulus plot: ability to create phase-locked fMRI timecourses (also available in MRIcron).</small></div>
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