I'm really gratitude for your help, the volume you provide is exactly what I
need. Just as you said, I don't have the need to view the t-test result on F99.
But, I'm pretty intereted in F99, and want to use it as my template in the
future, even not the study at hand. Just call me a curious person.
Donald McLaren provided the transformations from 112RM-SL to F99 and vice
versa, which is very helpful. But I still need F99 volume as reference volume
when I carry out the registration.
tangzhenc...@fingerpass.net.cn
Donna Dierker
?? 2014-07-22 22:41
Caret, SureFit, and SuMS software users
?? Re: [caret-users] How to load my own file by caret?
Do you mind my asking why you want to view your t-test result on F99, when you
have it registered to 112RM-SL? Why not use the 112RM-SL mean underlay?
Is this just for visualization, or is there some analysis you want to do?
It sounds like you need a volumetric registration between the 112RM-SL
anatomical volume and the F99 volume. It is possible that Donald McLaren has
already computed one.
The F99 volume in the old 2006 tutorial was in AFNI format. If that is the
volume you want, I converted it to NIFTI:
http://brainmap.wustl.edu/pub/donna/ATLASES/MONKEY/Macaque.F99UA1.LR.03-11.nii
login pub
password download
If you mean a different F99 volume, then point me to your source.
If you do end up computing a volumetric registration between these atlases,
then make sure your versions match in terms of what is or is not stripped
(e.g., neither has had eyes, hindbrain, or other structures removed).
Again, I would not be surprised if Donald McLaren has done this already.
On Jul 21, 2014, at 8:58 PM, tangzhenc...@fingerpass.net.cn wrote:
Hi, Donna!
Many thanks for your explanation.
To be correct, the 'individual volume space' shall be 'group volume
space', I don't known if the expression is appropriate. In tbss, I register
FA of each monkey to the best target (selected by tbss_2_reg -n).
The format of my 2 sample T test result is *.nii.gz. With Flirt of
FSL, I have ever registered the result to 112RM-SL, which is also of the
format of *.nii.gz.
Now, I want to register the result to F99 volume. But caret seems to
have a very different file format, I don't know which fle set as reference in
registration.
ChrisTang
tangzhenc...@fingerpass.net.cn
Donna Dierker
?? 2014-07-21 23:34
Caret, SureFit, and SuMS software users
?? Re: [caret-users] How to load my own file by caret?
Hi Chris,
See inline replies below.
Donna
On Jul 19, 2014, at 10:18 PM, ?? 1039537...@qq.com wrote:
Hi, everyone!
I process my monkey dti data on fsl, and have got 2 sample T
test result on individual volume space.
You say individual volume space. Does this mean the data is for a single
monkey? I guess I'm used to thinking two sample t-test is for two groups,
but I guess not necessarily.
I want to load my own result file as an overlay by caret and
set volume_F99 as underlay, so that I can estimate the brain areal of
significant.
You must use something like FSL's flirt or fnirt to register your
individual's anatomical scan (T1 or T2) to the F99 anatomical scan. I assume
your two sample t-test results are already in the same space as the T1 or T2.
If so, then apply that warp to your two sample t-test results.
Doing this will let you view your test results overlaid on F99, but it won't
say anything about significance. FSL's randomise should have said something
about this when you ran the two sample t-test. You can view these results in
fslview, too.
I know how to load a file and set it as an overlay, but I don't
know how to register it to F99 before that.
You need a tool that does volumetric registration (e.g., FSL's flirt or
fnirt). There are many others out there as well.
How can I realize that?
With thanks, ChrisTang
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