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Forum TrackVis Usage Weird loation of Loaded nifti ROIs

Weird loation of Loaded nifti ROIs
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1:50 am
May 8, 2010


Han

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Hi,

 

Thanks for providing this nice application to us.

 

I tried to load nifti format ROI into trackvis and the location is wrong. Before loading it, I register this ROI image (got from standard atlas) to a orignial tensor image and check this ROI is shown on the right location of the tensor image. However, when I loaded into trackvis along with fibers, its location is on the mirror location (if ROI is the frontal lobe, it is shown nearby the occipital lobe.) Using a dimension swap utility of FSL, I tried to change the direction of the axis, but still shown on the wrong location. What should I do? What is the coordinate of fibers?

 

Thanks in advance!

11:42 am
May 10, 2010


Ruopeng

Admin

posts 353
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Would it be possible to send me the track file and that ROI file? That would be very helpful.

Thanks,

Ruopeng

1:27 am
May 11, 2010


Han

Member

posts 8
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Hi, Ruopeng.

 

Great to hear that you can help me! How can I send the files?

 

Best,

Han

3:11 pm
May 11, 2010


Ruopeng

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Post edited 3:13 pm – May 11, 2010 by Ruopeng

You can file-drop it through here:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Use rpwang @ nmr.mgh.harvard.edu (remove spaces) as my email address.

Thanks,

Ruopeng

1:20 am
May 12, 2010


Han

Member

posts 8
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Thanks for your helps. I uploaded files.

 

Best

Han

12:26 pm
May 14, 2010


Ruopeng

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Post edited 12:27 pm – May 14, 2010 by Ruopeng

Thanks for the data. There are a couple of problems:

First, the track looks wrong. You need to apply one of the "invert" options at tracking step.

Secondly, the b0 nifti file does not have any coordinate rotation matrix information. As you can see in trackvis, orientations annotations are all wrong. But the roi file does have it. Can you tell me what the original form of your raw data? Are they dicom?

Ruopeng

6:56 pm
May 16, 2010


Han

Member

posts 8
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Post edited 7:30 pm – May 16, 2010 by Han

Good afernoon,

 

Got it, Those were problems. The original file was Nifti format. So DTK uses rotation matrix information of the orignial data.  I checked other data and they were fine!

Thank you so much.

 

Best,

Han

 

 

 
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