brain
Assume CON14 is our subject ID and it is inside directory $SUBJECTS_DIR. After the display window and the control panel pops up, try playing with the menus and buttons. tkmedit for volume tkmedit CON14 rawavg.mgz tkmedit CON14 rawavg.mgz lh.pial -aux
recon-all is a batch program and runs >30 steps. It easily takes 30 hours to finish one subject. Use tkmedit CON14 T1.mgz and tksurfer CON14 lh inflated to visualize images. More about visualization with freesurfer. Note: commands are in green. T
Hardware settings In the “Projector source” panel, click “eprime” button to select Eprime as source. Always turn the knob to “SRBox” instead of “USBox”. Transfering data: You use gFTP to transfer data f
E-Prime This piece of code is used in Lucas Center scanner #2 at Stanford University. SRBOX.Lamps "4" Sleep(100) SRBOX.Lamps "" Set SumACC = New Summation You also need to declare SumACC in user script Dim SumACC = As Summation Ma
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
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
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
/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.
