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Forum Diffusion Toolkit Usage FA is not created

FA is not created
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4:41 am
April 13, 2010


ann

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Hello,

I am recently facing this problem where the FA map is not created by dtk any more.I'm reconstructing DSI data with 514 directions.

 

I obtain the odf, max, dwi, trk but not the fa as before…..

 

Thank you for your help,

 

 

12:54 pm
April 14, 2010


Ruopeng

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Post edited 4:56 pm – April 14, 2010 by Ruopeng

I removed it in the latest releaseFrown because it relies on a pre-calculated fitting matrix. That is just not pretty. Sorry.

If you really need it, you can reconstruct the data as DTI data with multiple high b values. I've uploaded the gradient table for dsi 514. You can use it to reconstruct your DSI data as DTI. Make sure to check "multiple high b values" when you do that.

dsi514.txt

3:58 pm
June 14, 2011


Koene Van Dijk

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Post edited 1:43 pm – June 15, 2011 by Koene Van Dijk

Let's see if I can wake up this thread:

 

Hi Ruopeng,

I'm having the same problem as the original poster but I have 124 direction DSI data and not 514.

1. Would you have the gradient table for a 124 direction DSI scan? 

2. You mentioned above "reconstruct your DSI data as DTI". Do you mean I should choose DTI in the gui? And what b0 value should I choose?

3. You said above: "Make sure to check 'multiple high b values' when you do that". Is that an option in the gui? I cannot find it.

 

Thanks,

Koene

PS: I'm using trackvis-0.4.4/bin/dtk on a linux box

11:13 am
June 15, 2011


Ruopeng

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Hi Koene,

You can get the 124 gradient table here:

http://trackvis.org/dtk/raw124.txt

To reconstruct it as DTI, just select DTI model, check "multiple high b values" and set the b value which will be treated as the maximum b value in this case.

You need the latest dtk for that. Your version 0.4.4 is too old.

Ruopeng

1:56 pm
June 15, 2011


Koene Van Dijk

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Ruopeng:

thanks for the quick reply!

ah: I've updated the software and indeed now see the options you mentioned. It seems to work: I'm getting the "DTI" ouput files, such as FA map.

One thing: you said "set the b value which will be treated as the maximum b value in this case". To what should I set the b value? Default was 1000. Is that OK for this DSI_BCC124 protocol?

-Koene

11:33 am
June 17, 2011


Ruopeng

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It should be set as the maximum b value for the DSI scan. But if you only care about the FA maps or the relative values of ADC, it doesn't really matter.

Ruopeng

11:52 am
June 17, 2011


Koene Van Dijk

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forgive me my ignorance but I don't know what "the maximum b value for the DSI scan" is. Where can I find that?

-koene

1:57 pm
June 17, 2011


Ruopeng

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Post edited 5:57 pm – June 17, 2011 by Ruopeng

Whoever did the scan should know.

Ruopeng

2:01 pm
June 17, 2011


Koene Van Dijk

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Post edited 6:02 pm – June 17, 2011 by Koene Van Dijk

ah… Well, I do have the protocol from the Siemens scanner and it says this among others:

- – – – – – – – – – – – – – – – -

Diffusion mode MDDW

Diff. weightings 2

b-value 1 0 s/mm²

b-value 2 7000 s/mm²

Mosaic On

Noise level 20

Diff. directions 124

- – – – – – – – – – – – – – – – –

 

So I guess the answer to my questions is: 7000 ?

2:13 pm
June 17, 2011


Ruopeng

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That should be it.

2:14 pm
June 17, 2011


Koene Van Dijk

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thanks!
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