Thanks for the reply Tim,
I’m having trouble getting them to open in wb_view. Running out of memory even
when I request 60G, though the files themselves are 4.2G. There’s only 1
overlay in the red-yellow palette there and it’s overplayed over the
MNI152_T1_2mm template. I think it looks like multiple overlays because of the
parcel smoothing with the FSL structseg restricting the smoothing to cortex,
CSF, sub-cortex etc.
I don’t think there are NaNs in my data because I used -fixnan 0 in my call to
-volume-math when demeaning and normalizing (see below). Is there an easy way
to check for NaNs with workbench, or do I have to read it into Matlab?
When I do -volume-smoothing with -fix-zeros I don’t get holes but I do get
dilation. Guessing I can fix this by including a brain mask with -roi though.
That may be sufficient for my needs right now, though I’m confused why that
doesn’t fix it with the parcel smoothing.
I did use -exclude-outliers 3 3 in calling -volume-reduce to make my mean and
stdev images, which I thought would be important for removing background that
appear to be 0, but maybe I’m mistaken and this is the source of my problem?
demeaning and variance normalization:
wb_command -volume-math '(x-mean)/stdev’ \
${subID}_demean_${run}_hp2000_clean.nii.gz \
-fixnan 0 \
-var x ${run}_hp2000_clean.nii.gz \
-var mean mean_${run}_hp2000_clean.nii.gz -repeat \
-var stdev stdev_${run}_hp2000_clean.nii.gz -repeat
Best,
Jared
> On Feb 23, 2017, at 4:17 PM, Timothy Coalson <[email protected]> wrote:
>
> The -fix-zeros options are basically designed to to dilation into regions of
> zero values, so you probably shouldn't be using it.
>
> Maybe your input data has NaN values in it? That would lead to holes that
> expand with the smoothing kernel (but should have cube shapes, so it doesn't
> quite seem to fit your images).
>
> I also don't know what causes fslview to draw a "hole", so there might be
> other possible causes - see what it looks like in wb_view. I'm also not sure
> exactly what you are overlaying in those images, it almost looks like the
> first one has more than one image overlaid in the red/yellow palette.
>
> Tim
>
>
> On Thu, Feb 23, 2017 at 12:21 PM, Jared P Zimmerman
> <[email protected] <mailto:[email protected]>> wrote:
> Hi HCP users,
>
> I’m having a problem smoothing volume data with workbench, where both
> -volume-smoothing and -volume-parcel-smoothing are creating holes in my data.
> See the attached screenshot for an example. I’ve tried both with and
> without -fix-zeros and this fixes the holes for -volume-smoothing, however it
> also seems to dilate my image so that it becomes ~120% the size it should be
> (image also attached). Parcel smoothing seems to fix the dilation problem,
> but it still introduces holes in the data regardless of whether the -fix-zero
> flag is used. For my parcels I’m using FSL’s MNI152_T1_2mm_structseg.nii.gz
> as a first pass. Any idea as to why these holes are popping up?
>
>
> <Screen Shot 2017-02-23 at 12.53.24 PM.png>
>
>
> <Screen Shot 2017-02-23 at 1.06.49 PM.png>
>
>
> thanks,
> Jared
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