brain

spm_get, spm_select, and char

The mostly used functions I use in SPM is spm_get (for spm2) and spm_select (spm5 and 8).  These two functions are used to get files (usually image files). Frankly speaking I like spm_get much better as it’s intuitive and easy to use. Here is h
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1 min read

FSL environment setting

setenv FSLDIR /fs/quarry/cuixu/fsl41/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH}
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3 sec read

Famous brains

Text source: http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach Talairach brain (single) the brain dissected and photographed for the famous Talairach and Tournoux atlas. The atlas has Brodmann’s areas labelled, albeit in a rather approximat
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57 sec read

Conversion of coordinates between two images

Assume you have an image F and you identify a point (x,y,z) on this image (say with SPM’s display function). You then normalize this image F according to a template image G using SPM. Now you want to know that point’s corresponding coordi
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34 sec read

E-prime vs MatLab (+Psychophysics Toolbox)

Both E-prime and MatLab are popular tools for presenting stimuli for fMRI, NIRS and behavioral experiments. Here are a comparison between them. E-Prime MatLab + psychophysics toolbox price ~$1000 MatLab cost, $50-500 easy to use easy moderate need co
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12 sec read

Use serial port to trigger ETG 4000 with E-Prime

Open properties of the experiment, select tab “Devices” Add a serial port. Make sure the COM Port number is correct In your experiment flow, add inline function to where you want to trigger ETG4000 or put marker. In that function, enter t
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14 sec read

xjView Tutorial Videos

FDR function, English version FDR function, Chinese version 普通话 Mandarin FDR function, Chinese versi
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2 sec read

Sensitivity, specificity, ROC, AUC …

You can’t believe how much jargon there is in binary classification. Just remember the following diagram (from wiki). accuracy = ( TP + TN ) / (P+N), i.e. correctly classified divided by the total false discovery rate (FDR) = TP / (TP+FP), i.e.
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1 min read