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FSL  August 2009

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Subject:

Re: Problems with GE's DTI acquisitions

From:

"Evangelou, Iordanis (NIH/NINDS) [E]" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 3 Aug 2009 12:28:08 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (77 lines)

Yes you do need the research key for that.

You need to be in research mode
After you download go to Research User CVs
And make the changes
 
-------------------------------------------------------------------
Iordanis E. Evangelou, DPhil, Eur Ing, MIET
Research Fellow
Neuroimaging Section
Neuroimmunology Branch
National Institute of Neurological Disorders and Stroke
National Institutes of Health
Building 10, Room 5C203B
Bethesda, MD 20892
USA
-------------------------------------------------------------------
 
" If we knew what it was we were doing, it would not be called research, would it? "
Albert Einstein

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rajeet Saluja
Sent: Friday, July 31, 2009 1:48 PM
To: [log in to unmask]
Subject: Re: [FSL] Problems with GE's DTI acquisitions

Hi Iordanis,

Thanks for the suggestion but unfortunately the only option we get on the CV is "DTI on or 
off".  I suspect it is because this is a clinical machine and we don't have a "research key".  
Do you, or anyone else, have any other ideas?  Should I try resampling the data?  If so, how 
would you do it? With FLIRT?

Thanks in advance!

Rajeet

On Thu, 30 Jul 2009 11:33:03 -0400, Evangelou, Iordanis (NIH/NINDS) [E] 
<[log in to unmask]> wrote:

>There are some user CVs on the GE scanner to turn off the imaging upsampling of any 
sequence
>
>rhmethod = 1
>rhrcxres = 128
>rhrcyres = 128
>
>iordanis
>
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rajeet 
Saluja
>Sent: Thursday, July 30, 2009 10:51 AM
>To: [log in to unmask]
>Subject: [FSL] Problems with GE's DTI acquisitions
>
>Hi,
>
>About a week ago, I had an issue with probtrackx that, thanks to Saad, we 
>were able to figure out had to deal with upsampling of our DTI images from 
>128x128 to 256x256 that occured with the GE MRI that we have at our 
>institution.  Unfortunately, after much leg-work including speaking to the 
>company rep, it seems that this is default at the time of acquisition and 
>cannot be turned off.  I tried a couple more scans and it seems that fsl is able 
>to process the scans if I use 5 mm cuts but not at 3 mm.  With 5mm cuts 
>however, the images are kind of crappy and it still won't let me use masks 
>created in structural space using my global T1 acquisition.  I'm currently 
>testing out 4mm but I'm not very optimistic.
>
>So, my question is, has anyone else run in to similar issues and, if so, how did 
>you get around it?  Are there ways of converting it back to 128x128 without 
>modifying the data acquired?  Thanks in advance...
>
>Rajeet

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