Maxprime

Higgs chaser
10+ Year Member
5+ Year Member
Nov 28, 2005
2,125
7
Status
Medical Student
For those that work with MRI, what software packages do you guys use? I'm trying to automate skull stripping and the best I've come across is BET2 in the FSL package . . . which only runs on *nix machines. :( I am also curious what people use for DTI - I thought that Asclepios looked most promising. Here's what I use, please tell me where I'm wrong:

Normalization: SPM
Viewing/VOI & ROI creation/etc.: MRIcroN
Voxel Based Morphometry: NPM (part of the MRIcroN package)

Any suggestions?

(BTW, I don't need commentary about how awful I am for being stuck on Win32 - it's out of my hands.)
 

Jorje286

Member
10+ Year Member
Jul 19, 2004
637
68
Status
I know that Brain Voyager is used in the lab I'm working in, but I've never done fMRI myself so I don't know what is exactly used for (other than it's for fMRI).
 

jsydc

10+ Year Member
5+ Year Member
Feb 22, 2008
59
0
Status
Resident [Any Field]
A lot of the MINC tools are offered in some binary forms for windows. They aren't the most accessible, but probably the most robust. If you are planning on doing anything novel with the tools you use then I would advise running linux in a VMWare or other virtualization environment. I don't do DTI, but I do some VBM and DBM using a variety of the MINC tools. (Since they were developed here at McGill, I don't have much choice in the matter, but it's still a pretty good toolset for a lot of things.)
 

Neuronix

Total nerd
Staff member
Administrator
15+ Year Member
Mar 14, 2002
13,004
2,221
the beach
Status
Attending Physician
For those that work with MRI, what software packages do you guys use? I'm trying to automate skull stripping and the best I've come across is BET2 in the FSL package . . . which only runs on *nix machines. :(
BET is included in MRIcro (different from MRIcron) for Windows and I've used it just fine.

I am also curious what people use for DTI - I thought that Asclepios looked most promising. Here's what I use, please tell me where I'm wrong:
I use custom code written in IDL or Matlab for most of that sort of recon. For ROI drawing for volumes I use ITK-SNAP. I do some other ROI work in ImageJ and have written macros in ImageJ as well.

(BTW, I don't need commentary about how awful I am for being stuck on Win32 - it's out of my hands.)
I do everything in Win32 and I know how to use Linux quite well. There's nothing you have to do in *NIX these days for Image Recon as far as I can tell.
 
OP
M

Maxprime

Higgs chaser
10+ Year Member
5+ Year Member
Nov 28, 2005
2,125
7
Status
Medical Student
Good call on BET being in MRIcro - will definitely use that implementation. If ITK-SNAP does what it claims, that will be a HUGE help for ROI/VOI creation. What kind of things do you use macros for in ImageJ?
 

Neuronix

Total nerd
Staff member
Administrator
15+ Year Member
Mar 14, 2002
13,004
2,221
the beach
Status
Attending Physician
I use all kinds of ImageJ macros. The macro language is based around an even easier to program version of Java which I once knew very well and can still hack together. The essential macro I use time and time again is MeasureStack for through slice/temporal ROI drawing in properly arranged series. But, when it doesn't do exactly what I want, I make a macro. The macros I've written are for automatic ROI planning and measurement and when I want different information than what the default ImageJ macros can give you, such as one for "fat profiles" for example.

I've tried on numerous occasions to download new ImageJ plug-ins/macros, and I've found that for me it's easier to code my own than to figure out how someone else's works :laugh:
 
OP
M

Maxprime

Higgs chaser
10+ Year Member
5+ Year Member
Nov 28, 2005
2,125
7
Status
Medical Student
I wish I was - lots of talks I wanted to attend. I finally got some time now that classes are over, Matlab == my new hero.
 

dunkindona

Junior Member
7+ Year Member
15+ Year Member
May 13, 2003
44
0
Visit site
Status
I must put a plug in for AFNI. Bob Cox and his crew at NIH do a remarkable job at keeping all the programs relevant. There is a very steep learning curve, though.
 

czarrar

10+ Year Member
May 20, 2008
11
0
Status
For those that work with MRI, what software packages do you guys use? I'm trying to automate skull stripping and the best I've come across is BET2 in the FSL package . . .
AFNI (3dSkullStrip for anatomicals and 3dAutomask for functionals) and Freesurfer are both better than BET in getting good skull stripping. FSL can also do VBM analysis.


(BTW, I don't need commentary about how awful I am for being stuck on Win32 - it's out of my hands.)
you can always install linux along with a windows system, either through virtualization like VMware or installing it on another hard-drive and having it boot separetely.