[Mristudio-users] problems with gradients

Wed Oct 20 22:19:41 EDT 2010

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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>>
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