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12:18 pm
March 22, 2010
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Armen
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| Member | posts 25 |
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Post edited 4:32 am – November 8, 2010 by Armen
Is it possible to display an anatomical image (higher resolution) instead of the b0 in trackvis so it would be easier to draw the ROIs?
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12:56 pm
March 22, 2010
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Ruopeng
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Unfortunately no, everything has to be of the same geometry as the track files in TrackVis. However, you can register b0 to your anatomical image (you need to do that anyway to align them), and then use "Track transform" function to transform the track file to the anatomical space. Then you can work on the tracks in the anatomical space.
Ruopeng
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4:15 am
April 2, 2010
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aurely1310
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| Member | posts 9 |
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Hello,
I have some promblems with the opening of anatomical images in trackvis, could you help me please?
When I want to open an anatomical image (niftii extension), the top of the image is missing. It cannot come from the image itself : its opening in others programs doesn't show the problem…then, how can I solve this problem ?
Thank you very much!
Aurélie.
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10:00 am
April 2, 2010
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Ruopeng
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Hi,
Does the image has the same geometry as the DTI images (for example, dwi or b0 image)? If not, trackvis will resample it to DTI space, thus it may change the resolution or crop the image. In any case, if the anatomical image is not aligned to DTI image, it doesn't make much sense to overlay it in DTI space. You need to register it to your b0 or dwi map before loading it to TrackVis.
Ruopeng
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8:39 am
April 24, 2010
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Marcella
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I tried to use track_transform command in order to visualize a track (corpus callosum) in T1 anatomical space, but I have a problem.
I used SPM5 to find the tranformation from the b0 (source) to t1 (reference) and I create the transformation file T.mtx
Finally, I tranformed the CC (dwi space) into rCC (T1 space):
track_transform CC.trk rCC.trk –src b0.nii –ref t1.nii –reg T.mtx
I attach the image of the result  
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8:57 am
April 24, 2010
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Marcella
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| Member | posts 8 |
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here also the header informations of rCC.trk obtained with track_info and of t1.nii obtained with MRIcro
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10:40 am
April 26, 2010
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Ruopeng
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Post edited 3:53 pm – April 27, 2010 by Ruopeng
track_transform only takes fsl and freesurfer style registration matrix. Is SPM5's transformation matrix file compatible with any of them? Sorry I'm not too familiar with spm.
Ruopeng
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1:15 am
November 8, 2010
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Armen
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| Member | posts 25 |
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Post edited 6:17 am – November 8, 2010 by Armen
Hi Ruopeng,
I am having some trouble with this. I do the image registration from a B0 to anatomical image in FSL's flirt and use the registration matrix with track_transform. Everything works fine except the tracks are flipped in the y direction. The anatomical image imports with the correct orientation though. Any idea what is going on?
Thanks.
Armen
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9:44 am
November 15, 2010
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Ruopeng
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Sorry for the late response. Would it be possible to send the data set for investigation?
Ruopeng
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10:21 am
May 3, 2011
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fm_phd
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Hi,
I think I have some problems with overlying anatomical images on my .trk.
As you wrote, with FSL I co-registered the b0 image on the anatomical one and used the matrix produced to perform the track_transform, but still, when I open the anatomical over new traks, they seem to be tilted or rotated respect to the MPRAGE.
Does anyone knows if I'm missing some step?
Thanks in advance,
f.m.
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