[Mristudio-users] Need GE 3 tesla 25 direction DTI gradient tableplease, thanks

Mon Oct 25 04:00:15 EDT 2010

There in the header, i think

________________________________

Von: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Wu, Joseph
Gesendet: Freitag, 22. Oktober 2010 19:15
An: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Betreff: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient
tableplease, thanks

Hi 

Does somebody have GE 3 tesla  25 direction DTI gradient table that they
can forward to : jcwu at uci.edu?  That would be greatly appreciated. 

Thanks,

Joe

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li
Sent: Thursday, October 21, 2010 8:18 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] problems with gradients

Dear Susumu,

I have a quick question about the gradient table I got from the
gradient_table_creator

It gives me a table with the [0 0 0] and [100 100 100] at the bottom
which seems to be different than those sample gradient table I have from
DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips
systems do the b0 scan at the end instead of at the beginning now?

Thanks!

Xu

On Oct 20, 2010, at 10:19 PM, susumu mori wrote:

Hi Jill,

I'm second to SC. When you are using Philips, even if you thought that
you are using exactly the same parameters, you could end up in two
different types of the gradient tables; overplus on and off. This is not
recorded in the beginning of PAR file.

So my suggestion is, try the "overplus on" option of the table
calculator.

Also, if you find that you used "overplus on", you have to type in the
oblique angle information in the calculator. The angle information is in
the PAR file.

The reason you didn't get the tractography right is most likely due to
"+/-" signs of the gradient table you used. You can test "x/y/z flip"
function of the tractography to test it. The best way is to use the
gradient calculator, which should be able to sort out all the issues.

Susumu

On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill <JZwicker at cw.bc.ca>
wrote:

Further to this message, the ROI values I get are consistent with the
previous scans, so it is just the fiber tracking that I am suspicious
of...

Thanks!

________________________________

From: mristudio-users-bounces at mristudio.org
[mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill
[JZwicker at cw.bc.ca]
Sent: October 19, 2010 1:26 PM

To: DTI Studio, ROI Editor, DiffeoMap Questions/Support

Subject: Re: [Mristudio-users] problems with gradients

Hi Susumu and SC,

You previously helped me with a tensor calc issue (see below). I have
since used the gradient calculator and obtained more RAM, and have
successfully analyzed two scans. However, the remaining scans are not
processing properly (i.e., I do not get a proper colour map). In looking
at the PAR files, the parameters are the same as the first two scans,
with the exception of the rescale and scale slopes, window center and
widths, and diffision parameters (nothing that changes what I enter to
the online gradient table calculator). Since the gradient table I was
using didn't work for successive scans, I took the gradients from the
PAR file. This seemed to work, but the colours were reversed, so I
switched coloumns around and got a seemingly accurate colour map.
However, when I tried to fiber track, the CST seems too short and the
values are not consistent with what I obtained in the previous 2 scans.

So...I am unsure why the previous gradient table didn't work and I don't
think my trial and error method of getting a colour map is accurate. I
would be happy to send you the PAR files (off the listserv) if that
would help.

Thank you in advance for your guidance.

Jill

________________________________

From: mristudio-users-bounces at mristudio.org
[mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
[susumu at mri.jhu.edu]
Sent: September 1, 2010 6:25 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] problems with tensor calc

I suspect memory problem. 

Please use stricter threshold (like FA>0.3 and angle <30, for example)
to see if it works. If it works, then it's memory problem (I mean, you
need more memory).

You can also save eigenvector0 and FA, close DtiStudio, and redo fiber
tracking using the saved file. If you start from tensor calculation, you
have all the raw data in your memory.

32-bit operating system can allocate only 1-1.5GB memory. 64bit is much
better.

susumu

On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill <JZwicker at cw.bc.ca> wrote:

Thank you so much! After some trial and error, I figured out the correct
gradient table. I can now get a beautiful colour map, but I have a new
problem. The program crashes everytime I try to do fibre tracking. Any
suggestions?

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin]
Sent: Wednesday, September 01, 2010 10:56 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] problems with tensor calc

Use the following link for the gradient table calculation.
You need to get some information required to fill in from Par file of
your data.
If your data is not in ParRec format, get it first.

http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html

-SC.

On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill <JZwicker at cw.bc.ca> wrote:
> Hi DTI Studio users,
>
> I am relatively new to DTI studio and have been using successfully to
do
> tractography on infant brain data collected on a Seimens. I am now
trying to
> analyze child brain data collected on a Philips. I can get a clear
image,
> but as soon as I try a tensor calculation, the image quality degrades
> significantly (no matter what the background noise level I set it to).
I
> made gradient tables from the PAR file (forwards and backwards) and
also
> flipped the z as the tutorial suggests. Any suggestions on how I can
solve
> this problem?
>
> Thanks for your help.
>
>
>
> Jill Zwicker, PhD, OT(C)
>
> Postdoctoral Fellow
>
> Child & Family Research Institute
>
> Developmental Neurosciences & Child Health
>
> L408 - 4480 Oak Street
>
> Vancouver, BC  V6H 3V4
>
> Phone: 604-875-2000 ext 6805
>
> Fax: 604-875-3569
>
> jzwicker at cw.bc.ca
>
>
>
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