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
>
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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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