Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats,
because that will give you a robust maximum (i.e., if there are a couple
of voxels that are outliers with a very high value it won't take them into
account, which is probably a good idea here). Then use 20% of that robust
maximum as your lower threshold and voila, you have your ROI.
Best,
a.y
On Wed, 18 Feb 2015, Barbara Kreilkamp wrote:
Thank you very much Anastasia,
May I please check with you if what I am thinking of doing sounds correct?
I would use fslstats in FSL with the flag -R which gives me the maximum
value. For Forceps major I get a value of 200, 20% of this value would be
40, so then in the path.pd.nii.gz image I threshold every value below 40
away.
Is it fine to use the -R flag in fslstats (I do not believe I should use the
-r flag)?
Best wishes,
Barbara Anne
Usage: fslstats [-t] <input> [options]
-t will give a separate output line for each 3D volume of a 4D timeseries
Note - options are applied in order, e.g. -M -l 10 -M will report the
non-zero mean, apply a threshold and then report the new nonzero mean
-l <lthresh> : set lower threshold
-u <uthresh> : set upper threshold
-r : output <robust min intensity> <robust max intensity>
-R : output <min intensity> <max intensity>
On 17/02/2015 14:47, Anastasia Yendiki wrote:
Hi Barbara Anne - In each tract's directory, you'll find
the tract as a volumetric probability distribution in the
file path.pd.nii.gz. You can use that as an ROI to extract
statistics from any other volume that's in the same space
as the tracts (native DWI space). To be consistent with
the FA, MD, etc stats that are produced by default by
trac-all, you'd threshold path.pd.nii.gz to 20% of its max
value before using it as an ROI.
Hope this helps,
a.y
On Mon, 16 Feb 2015, Barbara Kreilkamp wrote:
Dear TRACULA experts,
I wonder if you could please assist me in
extracting tract values from an image I
transferred to diffusion space.
I ran TRACULA on my DTI dataset, however from
other structural images I aim to extract
values for tracts as well.
I also extracted DTI derived measures from
these tracts of my DTI data (FA,MD,RD,AD),
using this command: trac-all -stat -c dmrirc
And now I wonder whether I could add another
line to the source code of the stats
command so that it would output values from
that other image I have in diffusion
space.
Best wishes and thank you,
Barbara Anne
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