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FSL  March 2009

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Subject:

Re: Odd results from fslmaths and fslstats

From:

"Lindgren, Kristen, Ann" <[log in to unmask]>

Reply-To:

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

Date:

Thu, 26 Mar 2009 07:45:34 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (87 lines)

Thanks, Steve!  I just tried the command with "-odt float" and it worked perfectly.  You're the best!

Kristen (a very thankful student who's crunching her final set of dissertation data...)


-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Steve Smith
Sent: Thu 3/26/2009 4:11 AM
To: [log in to unmask]
Subject: Re: [FSL] Odd results from fslmaths and fslstats
 
I think this is a simple as:

If you start the fslmaths command with an integer image like fdt_paths  
the output will be integer. Hence you can't then mask a floating point  
FA image and output that; you need to add the final "-odt float"  
command at the very end.

Steve.




On 26 Mar 2009, at 01:08, Lindgren, Kristen, Ann wrote:

> Hey everyone.  I was wondering if anyone had any insight into why I  
> might be getting odd data after using fslmaths and fslstats.  Here's  
> what I've done so far.  Ultimately I'm trying to get the average FA  
> and volume of the resulting pathway from probtrackx:
>
> 1) Ran probtrackx using multiple masks (had two seeding points in  
> structural space) for each hemisphere using default values
> 2) Using ApplyXFM_gui, moved dti_FA to structural space (used  
> diff2str.mat as transformation matrix) - resulting file is called  
> dti_FA_str
> 3) Binarized fdt_paths and then multiplied it by dti_FA_str using  
> this command (note when I originally got advice on this way back  
> when I was told to use avwmaths_32R for this step but that doesn't  
> exist anymore so I used fslmaths)
>
> fslmaths fdt_paths -thr 50 -bin -mul dti_FA_str fdt_paths_values
>
> 4) Retrieved average FA and volume using this command
>
> fslstats fdt_paths_values -M -V
>
>
>
> So here's my issue.  This appears to work, although I've run into  
> some subjects where the output for average FA is 1.000000 while  
> still having a reasonable volume value.  I opened a subject's  
> dti_FA_str and added fdt_paths and fdt_paths_values.  There are 1) a  
> number of voxels that have intensities greater than 50 that are not  
> included in fdt_paths_values and 2) all the voxels in  
> fdt_paths_values have intensities of 1 (even though dti_FA_str has  
> clear values consistent with white matter FA).  I looked at the same  
> files in a subject where I got actual FA values and fdt_paths_values  
> looks much less patchy and appears to encompass all voxels greater  
> than 50.  What's odd is that for all but one subject, this seems to  
> only be happening in one hemisphere.  For instance, the last subject  
> I pulled, the data was fine for the left hemisphere but FA=1 came  
> out for the right hemisphere.
>
> I thought maybe somehow fdt_paths_values was getting binarized, so I  
> tried running fslmaths first with -thr and -bin and then running it  
> again with -mul, but I still get the same thing.  All the voxels in  
> fdt_paths_values still had a value of 1.
>
> Does anyone have any idea what's going on here and how to fix it?   
> Also, since I'm writing, I may as well check and see that people  
> still think using a threshold of 50/5000 is acceptable for this  
> analysis (connecting two masks that are known to be connected).
>
> Thanks in advance for your help.  Sorry for the long e-mail...
>
> Kristen
>


---------------------------------------------------------------------------
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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