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FSL  March 2007

FSL March 2007

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Subject:

Re: siena -sienax questions

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 24 Mar 2007 17:34:37 +0000

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (123 lines) , bet_robust (123 lines) , Unknown Name (17 lines)

Hi,

On 23 Mar 2007, at 19:02, Antonios - Constantine wrote:

> Dear fsl users,
> I used siena and sienax to process longitudinal and cross sectional  
> 25 data
> sets. Each data set consists of 2 T1 scans at 2 different  
> intervals. Both
> scans are of different FOV and quality. The first time interval's  
> scan is of
> 256x256x124voxels and 1.093x10.93x1.5mm voxel dimensions while the  
> other is
> of 256x256x50 and 1.093x1.093x 2.5mm.
> I had to process 10 data sets of Controls (with scans at 2different
> intervals ) and 15data sets of Parkinson Disease patients (with  
> scans at 2
> different intervals also) and, correct me if i'm wrong, i used the  
> same
> parameters settings for all the data sets in siena and sienax  
> respectively,
> in order to have an objective comparison of the results.
>
> In almost all of the data i had very good results except from 3  
> data sets.
> In these data sets the Bet tool failed totally, hence both siena  
> and sienax
> gave bad results and siena printed in 2 out of 3 datasets a warning:
> “Probably failed consistency, check for standard space registrations”
>
> I have the following questions:
>
> 1)what's the meaning of the siena's warning output? Cause i didn't  
> find any
> info about that in fsl's web page /lectures.

This means that the various registrations were not consistent between  
the two images, which means that at least one of them failed. Your  
two input images are quite different from each other so the value of  
running SIENA between them is rather questionable anyway I'm afraid.  
However....

In the example you sent the two images registered to each other ok,  
but the second image didn't register well to standard space - this  
may be because BET isn't working on this image with these options. I  
suggest that you use bet_robust (script attached) instead of bet in  
the siena script (take a local copy of $FSLDIR/bin/siena and change  
the bet calls near the start) and remove the BET options that you  
added before. You could probably turn off the -m option then as well.

This then runs through SIENA ok, but the images are also somewhat  
distorted relative to each other - I really don't think it's a great  
idea to use such different pairings in SIENA!

> 2)why i didn't have these problems in siena with the other data  
> sets , since
> all of them are of different quality and FOV ?

Presumably because FLIRT succeeded in those cases but not the more  
problematic ones.

> 3)If i change sienax parameters then i'll probably find a set that  
> will help
> Bet to succeed but if i'll do that then how can i compare the  
> results of all
> my data sets since the comparison won't be objective??

I'm afraid you can't really use SIENAX to compare between very  
different acquisitions, such as you have here. The segmentation  
output volumes almost certainly won't be comparable between  
timepoints, though you could just use the first OR second timepoints  
to compare volumes across subjects. In this case, if you hand-tune  
BET to work well across subjects such that it looks good in each, you  
are probably ok - though again you may find that bet_robust works  
better anyway without needing hand tuning.

> 4)Is it wrong that i used siena to make longitudinal analysis in  
> data that
> have different FOV, without reducing the FOV of the “bigger” image  
> till it
> reaches the “smaller” one?

Each pairwise analysis is ok - but you need to be careful that the  
results are comparable across subjects.

> 5)I used siena in all my data with the following set up: siena A B
> “parameters settings” where A is the scan with the smaller FOV and  
> less
> resolution (2.5mm ) and B the scan with the bigger FOV and higher  
> resolution
> (1.5mm). If i change the sequence of the scans in siena :siena B A
> “parameters settings” there is a difference in the PBVC. why is that?

In general this doesn't happen - in this case it's probably related  
to the standard space registration problems.

> 6)In some results i noticed that after segmentations the eyes were not
> excluded. does this induce a serious error in siena/sienax results?  
> and if
> yes how can i avoid that without changing the siena/sienax  
> parameters which
> will make the final results not objective for comparison with the  
> other
> results of my data??

Hopefully these issues will be helped by the above.

Cheers, Steve.


>
> Thank you once again for your valuable support
> Antonios-Constantine Thanellas
>
>
> P.S. I've uploaded one of the data sets where i had these problems  
> with the
> output of the siena script on these data. They are control data  
> from the
> same subject in different intervals. The ref ID is :377949




------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---

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