Hi
I did see that there was an artifacts (stripes) running across entire image in 2dseq of data1. And data 2 is fine to me. Looks like to me that it is not problem due to conversion, it was acquired with artifacts in data 1 (acquisition artifacts, I believe). Since your bruker system has built in modules to calculate volume of the injured area, What are you going to do with the data in FSL? Are you going to segment entire brain? Are you gonna combine all the animals from entire group and coregister it and calculate volume? If it is just calculate volume of injury, I would choose imagej to do that....
Thanks
Ned
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of SUBSCRIBE FSL Vasily
Sent: Monday, November 02, 2015 8:57 AM
To: [log in to unmask]
Subject: [FSL] Rat brain injury
Good time of a day, friends.
I'm faced with the necessity to analyze brain rat injury MRI images. And I am absolutely new to this work in general and FSL in particular. So if my questions are not bright, please excuse me.
I've got mri images of a rat brain. On the right side there is a lighter field of injury (I guess, you ll see it much better than I do). I need to get the volume of injury zone and volumes of both hemispheres.
Here is drop box link for MRI stack and 2dseq files.
https://www.dropbox.com/sh/l33m7d109a0o862/AAD9jY5JgZtyt1toxHBNbWGya?dl=0
For now I have the most simple idea (how my older colleagues are doing) to manually select area on all slices (on tiff in imageJ) and than calculate volume by hands (in excel).
And it seems... not so optimised way to me.
I have tried to convert it to dicom than to nfii. And to analyze it in fsl, but somewhere between this steps something went wrong and images where fully corrupted.
And because I am completly new I dont know where to look for troubles.
So. If you can give some advices like "this 2dseq files are broken - try to get better" or "it works bad on rat - do in in imageJ", or "it worked all right for me, so try harder and you will get what you want" it will be very helpfull. It's much easier to work when you know it can give results.
If you can give me some other advices (maybe about other programs or exact steps of what to do - I'll be even more thankful, but of course I'm trying to find it out myself anyway).
Thank you a lot for your time
Vasily
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