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6:32 am
June 17, 2011
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r.navarra
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| Member | posts 13 |
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We have many DTI data (from Philips 3T, standard low, medium, high and experimental 60s directions). By using default paremeter values in Diffusion Toolkit We get good FA images but when We try to track fibers, our results are very poor: short or nothing fibers from even real big ROIs. We did try to change angle and mask threshold, orientation path and propagation algorithm but it dosn't work yet. 
 
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11:36 am
June 17, 2011
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Ruopeng
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A slice filter was automatically applied when you load the tracks. So what you see is only tracks from that slice. You can uncheck it to see everthing (slow!). Maybe you should take a look at the demos which explains those things.
http://trackvis.org/demo/
Ruopeng
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12:29 pm
June 20, 2011
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r.navarra
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| Member | posts 13 |
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Post edited 4:30 pm – June 20, 2011 by r.navarra
Thanky you for reply. I've seen demos.
I think the problem is the length of the fibers. With my data is always very low (short) and also by setting manually I get the abnormal fibers. I'm afraid of committing a mistake in the DTK execution or settings but I do not know how to control, the FA corresponds with that one that I obtain with FSL.
First picture is from our data. Second one from a workshop ( http://www.ismrm.org/italy/Ima…..natomy.pdf )
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11:04 am
June 21, 2011
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Ruopeng
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The tracks in the first picture do not appear right. But I can't really tell from a static picture. If you could send me the track file or even the raw image data, I should have a better idea.
Ruopeng
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2:26 pm
June 22, 2011
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r.navarra
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| Member | posts 13 |
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Thank you so much for support!
All data is in: http://www.megaupload.com/?d=RF7M3MKP
PAR/REC files are original data.
NifTI files are:
dataorig : from dcm2nii
dataDTI : il dataorig without last volume (mean of gradient volumes)
DTIgtcX files are:
Gradient tables from PAR/REC by using DTI_gradient_table_creator_Philips_RelX
DTK_bvecs.txt:
Gradient table for DTK (0,0,0 in last position)
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12:12 pm
June 29, 2011
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Ruopeng
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Sorry for the late reply. I'm having trouble accessing megaupload website from work. Would it be possible to send it through here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Please zip everything to one file and use rpwang@nmr.mgh.harvard.edu as my email address.
Best,
Ruopeng
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3:19 am
June 30, 2011
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r.navarra
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| Member | posts 13 |
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Post edited 12:51 pm – June 30, 2011 by r.navarra
Uploading… Done! :)
Thank you.
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11:36 am
June 30, 2011
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Ruopeng
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Got it. It appears that you just need to apply a "Invert X" in tracking step. It often happens with diffusion data from different scanners or different "eras". You just need to play with the inversion flag and see what makes best sense.
Best,
Ruopeng
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12:40 pm
June 30, 2011
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r.navarra
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| Member | posts 13 |
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UHUU! It works!!!! :D Thank you so much! 
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