brain

xjView, a viewing program for SPM2, SPM5, SPM8 and…

xjView’s official webpage moves to https://www.alivelearn.net/xjview/ xjView is a MatLab program Jian and I wrote a few years ago to display SPM T-test images more easily. Main features include p-value slider: change p-value and display the sup
Xu Cui
33 sec read

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
Xu Cui
2 min read

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
Xu Cui
1 min read

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.
Xu Cui
8 sec read