[Mristudio-users] Fiber tracking after updating in landmarker

[Priti Srinivasan]

Hi All,

My goal is to do fiber tracking after registering my target to the MNI template and as per your advice I did the following.

1. Created and the tensor.d file from the Dtimap tab in DTI studio. 
2. Registered the tensor image to the MNI space in Landmarker.
3. Saved the updated tensor image.
4. Re-opened DTI studio and opened a DWI image (not warped to the MNI template) and used the open.d option and opened the tensor image to recalculate all the vectors, ADC and FA images

Result: White lines against a black background.

5. Re-opened DTI studio and opened a DWI image (that was warped to MNI template using) landmarker and used the open.d option (as I assumed it must have been a problem with the dimensions) to recalculate my images 

Results: Weird images not like the one before but it looked more like a distorted image matrix. All the recalculated images looked like this.

Any suggestion on where I am going wrong?

Thanks,

Priti




Good question. It is a bit complicated because you can't open a tensor file
directly by DtiStudio. 

1) First you need to open a scalar image file such as FA, ADC, DWI, b0 with
the same image dimension. Usually one of those images of the same subject.

2) Once you get the image opened in a viewing window, you can find the
"Open.d" button at the right column. Click this button.

3) A new dialog window shows up. Make sure that all the dimensions and voxel
sizes are correct and specify the "DtiStudio" format.

4) Don't forget to click a check box saying "Get eigen-value/vectors,,,,".
Specify the file name.

5) Click "ok". This will load your tensor file and recalculate all the
scalar images and vector images.

Please let me know if you have any question.

-----Original Message-----
From: JULIE E MCENTEE [mailto:jmcentee at jhmi.edu] 
Sent: Friday, April 04, 2008 10:21 AM
To: susumu at mri.jhu.edu
Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker

How do I read the (updated?) tensor file into DtiStudio?

Thanks- Julie

Julie E. McEntee, M.A., C.C.R.P.
Senior Research Program Coordinator
Department of Psychiatry- Neuroimaging
Johns Hopkins University School of Medicine
600 N. Wolfe St./ Phipps 300
Baltimore, MD 21287
Phone: 410-502-0468
Fax: 410-614-3676

----- Original Message -----
From: susumu <susumu at mri.jhu.edu>
Date: Thursday, April 3, 2008 6:00 pm
Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker
To: "'DTI Studio, ROI Editor,	Landmarker Questions/Support'"
<mristudio-users at mristudio.org>


> Hi Julie,
>  
>  When you got "white lines against black background", it's most likely 
> a
>  wrong image matrix. Please make sure that you load the data as a "vector"
>  file. Also, after the normalization to ICBM-MNI, all image should be
>  181x217x181. So, if you got the vector file transformed correctly, you
>  should get this matrix size after you select "vector" as the file format.
>  
>  There is one important issue, though. We don't recommend any
transformation
>  of vector files. This is because vector transformation is very 
> unstable. If
>  you want to do tracking after DTI image transformation, I strongly
suggest
>  to use "tensor transformation", not FA and vector transformation.
>  
>  This is simple. You need to open a tensor file using the "open .d"
button.
>  Then you can apply the AIR transformation matrix.
>  
>  Once your tensor is normalized to ICBM, your can read the transformed 
> tensor
>  file to DtiStudio and recalculate all the FA, ADC, vector things.
>  
>  Please let me know if you have further question.
>  
>  Susumu
>  
>  -----Original Message-----
>  From: mristudio-users-bounces at mristudio.org
>  [ On Behalf Of JULIE E MCENTEE
>  Sent: Thursday, April 03, 2008 5:06 PM
>  To: mristudio-users at mristudio.org
>  Subject: [Mristudio-users] fiber tracking after updating in Landmarker
>  
>  I normalised my Air.fa image to the ICBM-MNI-FA template using 
> Landmarker. I
>  am now trying to do fiber tracking (whole brain) using the Updated_Air.fa
>  image in DtiStudio. The only way I was able to get DtiStudio to do 
> the fiber
>  tracking was to normalise the eigenvectors (0, 1, 2) to the ICBM-MNI-FA
>  template in Landmarker, but then I am only able to load one 'updated'
>  eigenvector as the Principle Vector in DtiStudio. The result is some 
> white
>  lines against black background.
>  
>  What should I be doing here?
>  
>  Thank you for your help!
>  
>  Julie E. McEntee, M.A., C.C.R.P.
>  Senior Research Program Coordinator
>  Department of Psychiatry- Neuroimaging
>  Johns Hopkins University School of Medicine
>  600 N. Wolfe St./ Phipps 300
>  Baltimore, MD 21287
>  Phone: 410-502-0468
>  Fax: 410-614-3676
>  _______________________________________________
>  Mristudio-users mailing list
>  Mristudio-users at mristudio.org
>  
>  _______________________________________________
>  Mristudio-users mailing list
>  Mristudio-users at mristudio.org
>   





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