[Mristudio-users] problems with gradients

[Seongjin]

You may check a few options.

1. Overplus is on or off (make it sure with your examcard if it was on or
off.)
2. If b=0 image comes first or last in your DTI acquisition order.
3. DTI input fields are correctly filled out.
...

-SC

On Tue, Oct 19, 2010 at 4:26 PM, Zwicker, Jill <JZwicker at cw.bc.ca> wrote:

>  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<http://godzilla.kennedykrieger.org/%7Ejfarrell/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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>> >
>> >
>>
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>
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