[Mristudio-users] color coded maps

[susumu mori]

ColorMap0 is equal to EVec0 x FA
This is what people use. The assignment of the color; x = red, y=green,
z=blue is arbitrary, but this scheme is most widely used.

ColorMap1 is EVec1xFA
ColorMap2 is Evec2xFA

These are rarely used.

ColorMap0 is used for visual evaluation and rarely used for quantification
purpose.
As a matter of fact any EVec are rarely used for quantification purposes
except for tractography.


On Wed, Apr 10, 2013 at 11:31 PM, skhekmat <skhekmat at hotmail.com> wrote:

> One quick question, which color coded orientation map is important for
> display? It creates three color map files after tensor calculation,  (
> Looks same as when I create by multiplying eigen vector with FA map). I
> have seen people displaying different color coded maps . What is proper
> representation of directional coded FA map?****
>
> ** **
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori
> *Sent:* Wednesday, April 10, 2013 3:05 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] saving gradient file****
>
> ** **
>
> I simply save it as a text file and cut&paste.****
>
> You can also try *.dpf format.****
>
> ** **
>
> On Wed, Apr 10, 2013 at 1:22 PM, skhekmat <skhekmat at hotmail.com> wrote:***
> *
>
> Hello DTI Studio users****
>
> Is there any way to save my own gradient file(s) on the computer?****
>
> Thanks****
>
> Ned ****
>
>  ****
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *skhekmat
> *Sent:* Friday, April 05, 2013 2:02 PM
> *To:* 'DTI Studio, ROI Editor, DiffeoMap Questions/Support'
> *Subject:* Re: [Mristudio-users] masking****
>
>  ****
>
> Hello Susumu****
>
> Thanks for providing suggestions, I tried to follow that, I do have some
> questions on that…****
>
>  ****
>
> *From:* mristudio-users-bounces at mristudio.org [
> mailto:mristudio-users-bounces at mristudio.org<mristudio-users-bounces at mristudio.org>]
> *On Behalf Of *susumu mori
> *Sent:* Thursday, April 04, 2013 5:34 PM
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] masking****
>
>  ****
>
> Hi Ned,****
>
>  ****
>
> The simplest masking you can use is the intensity threshold.****
>
> When you click "tensor" calculation, there is a section to define an
> intensity threshold. This should suppress most of the background noise
> floor.****
>
> My question is, In DTI map option ( in tensor calculation) does it create
> and save a mask file  using threshold option 10 %) somewhere explicitly in
> my computer? If so, I could not find it.****
>
>  ****
>
>  ****
>
> More sophisticated method is to apply for skull-strip.****
>
> You can do this at the tensor calculation by loading a masking file,
> again, within the tensor calculation window.****
>
> The brain mask file should contain 1/0 information. ****
>
>  ****
>
> Using this option,  I created a roi mask file in binary format and but
> unable to load at tensor calculation, may be it reads only rec file****
>
> Or, you can skull-strip after tensor calculation.****
>
>  ****
>
> Using this, is a better option, after tensor calculation, I do not know
> how to apply to resultant images. ****
>
> For the skull-strip, you can use any software out there. We use our own
> skull-strip function in RoiEditor.****
>
> You can load FA, trace, and other images with b0 or iDWI (the sum of all
> DWIs you can calculate in DtiStudi).****
>
>  ****
>
> You can use b0 or iDWI for skull stripping and the resultant masking is
> applied to all loaded images.****
>
>  ****
>
> Hope this will help.****
>
>  ****
>
> Susumu****
>
>  ****
>
> On Thu, Apr 4, 2013 at 12:34 PM, skhekmat <skhekmat at hotmail.com> wrote:***
> *
>
> Hello All****
>
> Is there any function to create a mask in DTI studio, so that I will apply
> in Tensor mapping? I could create using other softwares, however,
> transformation causes so many issues.****
>
> Thanks****
>
> Ned****
>
>
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>  ****
>
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