I agree with David, but what are all the parameters of your diffusion sequence?

 

Peace,

 

Matt.

 


From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of David Gutman
Sent: Friday, December 11, 2009 9:59 AM
To: [log in to unmask]
Subject: Re: [FSL] noise or artifacts

 

Ok---  if possible in the future I'd try and collect at least 3-4 B0 images and average them prior to doing dtifit/DTI analysis. I think the rule of thumb is ~ 1 B0 for every 10 gradient directions collected.


Have you looked to see how "noisy" just your nodiff_brain image is?  Also are you just acquiring a single average (which is what I am guessing)...

On Fri, Dec 11, 2009 at 10:55 AM, Jiansong Xu <[log in to unmask]> wrote:

Hi, David:

 

Thanks for your comments. We acquire one B0 and 32 DTI weighted images. 

 

Best Regards

 

Jiansong

 

===============

Jiansong Xu, M.D., Ph.D.

Dept. of Psychiatry

Yale Medical School

2 Church St., Suite 215

New Haven, CT 06519

203-785-5306

 

 

 

 

 

 

On Dec 11, 2009, at 10:29 AM, David Gutman wrote:

 

How many B0 images are you collecting/averaging?   I think Saad or Maat can provide some more input-- but I distinctly remember at some point back people were noticing similiarly "high" intensity FA voxels--- if there's a lot of noise in your B0 image in particular, since it's used for a lot of the other calculations, if you have any "Noise" bits there it can cause some of this.  So collecting more B0 images and having a less "noisy" reference image for your calculations can be helpful.      Also are you getting many of the noise "bits" near CSF/gray/white junctions and/or near the surface of the skull?  They look pretty well distributed, but obviously hard to judge the intensity of some of them from a static 2D image...


On Fri, Dec 11, 2009 at 10:21 AM, Jiansong Xu <[log in to unmask]> wrote:

Dear All:

 

Some of my FA maps show a lot of randomly distributed high intensity voxels. Please see attached FA maps for example. My first impression is that these high intensity voxels indicate high level noises. Recently, I used the Local Noise Field Estimate Tool developed by Dr. Landman to measure the noise level of each DTI scan. Most subjects showing this type of "noisy" FA map also showed high level noise, but some of them also showed noise level lower than subjects showing good FA maps. Could any one comments on this inconsistent finding? Are these high intensity voxels caused by high level noise or any artifacts?



 

 

<Picture 2.png>  <Picture 3.png>

Best Regards

 

Jiansong

 

===============

Jiansong Xu, M.D., Ph.D.

Dept. of Psychiatry

Yale Medical School

2 Church St., Suite 215

New Haven, CT 06519

203-785-5306

 

 

 

 

 

 




--
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine

 




--
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine