Before using GIFT to do ICA analysis on your fMRI data, you need to do several pre-processing steps:
(1) slice timing correction (before realignment if your data were collected interleave fashion, otherwise after realignment) - This step is sometime neglected in the block design. For event-related design, it is important.
(2) realignment: get your motion parameters (x,y,z, roll, pitch, yaw)
(3) coregistration - T1-template, then apply transformation matrix to EPI.
(4) segmentation - skull stripping
(5) normalization - normalize to template
(6) smooth - blur the data
You can use spm_jobman('run',jobs) to do batch scripting. Save you time for group analysis.
Sunday, September 23, 2012
Recent - play with SPM and GIFT
Learned to use SPM for fMRI data analysis and GIFT for group ICA analysis.
Wrote some scripts for that.
If you're interested, please feel free to email me.
========= side story ========
9.23.2012
Afternoon
I was so scared when my laptop went to blue screen. I took the hard disk out and use external enclosure to plug it into my desktop. One partition became unallocated. Jesus! My important data were in that partition. When I almost lost my hope, I found a free software which called testdisk (http://www.cgsecurity.org/wiki/TestDisk). It fixed the partition table of my hard disk. My lost unallocated partition was found. THANKS my LORD. At the end, I saved my data. I am very thankful for GOOGLE and whoever made this little tool (testdisk). Otherwise, I am not sure if I can recover my data. Cheers! I donated a little money to the project (testdisk) for supporting their future development. Nice job!
Wrote some scripts for that.
If you're interested, please feel free to email me.
========= side story ========
9.23.2012
Afternoon
I was so scared when my laptop went to blue screen. I took the hard disk out and use external enclosure to plug it into my desktop. One partition became unallocated. Jesus! My important data were in that partition. When I almost lost my hope, I found a free software which called testdisk (http://www.cgsecurity.org/wiki/TestDisk). It fixed the partition table of my hard disk. My lost unallocated partition was found. THANKS my LORD. At the end, I saved my data. I am very thankful for GOOGLE and whoever made this little tool (testdisk). Otherwise, I am not sure if I can recover my data. Cheers! I donated a little money to the project (testdisk) for supporting their future development. Nice job!
Monday, September 10, 2012
Autum semester starts ~~~ my fourth year of my Ph.D. study!
8.27.2012 UC starts 2012 Autumn semester
Time really flies. Looking back my old plan, I should have been writing my thesis. I am still working hard and trying to figure out my fusion techniques. Three first-author papers have been published since I entered UC BME graduate program. My mentor Dr. Holland helped me tremendously in all aspects. Well, I still have quite a lot to finish up before I can graduate. Shoot for 2013 Summer or Autumn semester! Work hard to graduate soon.
Our new Ubuntu server:
(1) How to mount:
wan9vj@irc-maximus:~/yymnt$ mount-cifs-wrapper //pnrc-xserve.chmccorp.cchmc.org/language xlang -o uid=wan9vj,gid=`id -gn wan9vj`,sec=krb5
(2) Install CTF software packages on Ubuntu
Copy bin; lib etc., folders to your local folder, for example, ~/ctf folder. Then added that folder to your PATH (e.g. ~/.bashrc: export CTF_DIR=~/ctf export PATH=$PATH: ~/ctf/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: ~/ctf/lib). Then, you need to install some libraries accordingly. This is the hard part. Different machines and systems might have different requirements.
Currently, CTF software packages only work well under 32-bit system. They do not support 64-bit system. You can install 32-bit Linux inside of 64-bit Linux to go around this problem. Not fun though.
Time really flies. Looking back my old plan, I should have been writing my thesis. I am still working hard and trying to figure out my fusion techniques. Three first-author papers have been published since I entered UC BME graduate program. My mentor Dr. Holland helped me tremendously in all aspects. Well, I still have quite a lot to finish up before I can graduate. Shoot for 2013 Summer or Autumn semester! Work hard to graduate soon.
Our new Ubuntu server:
(1) How to mount:
wan9vj@irc-maximus:~/yymnt$ mount-cifs-wrapper //pnrc-xserve.chmccorp.cchmc.org/language xlang -o uid=wan9vj,gid=`id -gn wan9vj`,sec=krb5
(2) Install CTF software packages on Ubuntu
Copy bin; lib etc., folders to your local folder, for example, ~/ctf folder. Then added that folder to your PATH (e.g. ~/.bashrc: export CTF_DIR=~/ctf export PATH=$PATH: ~/ctf/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: ~/ctf/lib). Then, you need to install some libraries accordingly. This is the hard part. Different machines and systems might have different requirements.
Currently, CTF software packages only work well under 32-bit system. They do not support 64-bit system. You can install 32-bit Linux inside of 64-bit Linux to go around this problem. Not fun though.
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