# Xu Cui

## retinotopy with freesurfer

Retinotopy analysis consists two parts, one on high resolution structural images (segmentation, inflation, cut, etc), the other on functional images. structural Before you start, you need to put the structural i

## brain images: convert between different formats

For single file to single file conversion, you usually use mri_convert of freesurfer. For example mri_convert x.img y.nii Other options would be LONI Debabeler or MRICro. Here are some special cases: multiple 3D ANALYZE to a single 4D Nifti: mri_conc

## I support PLoS

As an author, when you publish paper, you pay to the publisher; As a reader, when you read paper, you pay to the publisher; This is absolutely ridiculous! The research is done using tax payer’s money and tax payers have to pay to access the pub

## amfphp bug? Negative integer becomes big positive

In local actionscript, if you have an object like: o.x = 6; o.y = -5; Then send this object to remote server using amfphp, the object becomes o = 6; o = 4294967290; This could be a bug…

## sqlite: update id automatically in a relational table

Let’s say we have three tables: user, paper, userPaperRelation. user has columns id and username paper has column id and title userPaperRelation has columns userID and paperID. userID corresponds to the id in user table; paperID corresponds to

## fslmerge: convert 3D ANALYZE to Nifti

/fs/quarry/cuixu/fsl/fslmerge -t f I_???.* On my computer, it doesn’t convert to .nii file; but to a single img/hdr pair. This method won’t be used. Instead, I use freesurfer’s mri_concat now. See here.

## vim cheatsheet

http://www.tuxfiles.org/linuxhelp/vimcheat.html Author: Nana Långstedt < nana.langstedt at gmail.com >   Working with files Vim command Action :e filename Open a new file. You can use the Tab key for automatic file name completion, just li
I use jsMath to write mathematical equations in this blog. Here is an example This is inline equation (use slash parenthesis): $$\alpha+\beta\geq\gamma=\pi$$ This is one line equation (use double dollar sign \$\$…\$\$): \int {1\over x}\,dx =