Hi,there,
I wonder whether I can think that it is atrophy if the end point of the arrow lies inside the closed surface and that it is inflation if the end point of the arrow lies outside the closed surface.
If yes, how could I cope with the situation that there is a very small cluster of vertices of inflation near a large cluster of atrophy. It seems to me that it might be caused by miscorrespondence between corresponding vertices.
Is there any suitable threshold of cluster size after FDR correction?
A cluster smaller than the threshold is considered to be caused by noises and should be masked.
How many vertices are considered significant?
Yuanchao
--- 09年12月7日，周一, Mark Jenkinson <[log in to unmask]> 写道：
发件人: Mark Jenkinson <[log in to unmask]>
主题: Re: [FSL] several questions about the FIRST tool
收件人: [log in to unmask]
日期: 2009年12月7日,周一,下午5:42
Dear Hanjian,
This is actually not my personal mailbox - it is the FSL list.
I have been away from work for a few days.
Also, I am not familiar with other packages for displaying vtk files and I
do not know if there is a strict standard as to which orientation (for
the left-right handedness) they are normally displayed. We display
things consistently with FSLView, which involves flipping left-right
for "neurologically ordered" files (positive determinant of the qform
or sform matrix). Our vtk coordinates use an internal coordinate
convention and do not follow the nifti conventions. Hence I am not
surprised that you see a left-right flip given these two significant
conventions (coordinates and display in FSLView). So I would
not worry about this.
The arrows show the direction of the mean change between
groups. If they are tangential to the surface then the change
is along the surface and neither inward nor outward.
I would not use fslswapdim to correct registration *errors*!
It is appropriate to use fslswapdim on your original images
to either fix labelling problems (A-P,L-R,S-I) or to put the images
in a more familiar orientation (like the standard templates).
However, I would *NOT* run it *after* any analysis has been
done. If you have a registration error then you should try to
fix it by cropping the image to remove large amounts of neck,
checking the brain extraction, changing the search space or
even selecting a different cost function.
I hope this helps.
All the best,
Mark
On 4 Dec 2009, at 06:22, duhanjian wrote:
> Dear Mark,
> I am very sorry to mail this letter to you mailbox directly. Beacause I haved sent those questions to the FSL mail box several days ago, but nobody answer those questions. So I mail those questions to you. Could you do me a favour?
> I was confused by following the questions.
> 1.Using FIRST package, I tried to make group analysis in patients vs normal controls. I found there was group difference in left amygdala and other structures. I tried to visualize the difference using vtk by my self. In the uploaded figure, I showed the left amygdala using vtk and fslview respectively. To my surprise, they are different. It seems to me that my result is a mirror image of the result obtained using fslview. In addition, the result obtained using fslview is smoother. Since I loaded the same NS_L_Amyg1_Fthresh.vtk file, why are the different in that way?
>
> 2.In addition, there are arrows which are tangent to the surface but the arrow is still outside the surface or inside the surface.Can we say that it is atrophy if the arrow lies inside the surface, no matter it is pointing inward or tangent to
> the surface?
>
> 3.In order to correct registration errors, I used fslswapdim command. What is the effect of fslswapdim? Should I take any additional steps when making group analysis if I performed the fslswapdim command?
>
> By the way, I have uploaded the pictures to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi. The six-digit reference number for this upload session is 555243.
>
> Thank you very much! Mark
>
>
>
> 2009-12-04
> yours sincerely,
> hanjian du
> Department of Neurosurgery, Southwest Hospital, Chongqing 400038, China
>
> 重庆市西南医院神经外科
> 杜寒剑
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