Thanks Tim, I’ll check for NaNs and try viewing in other viewers to make sure it’s not just a thresholding thing. Will try other segmentations too, though the one I’m using has full brain coverage, so I think the holes shouldn’t be caused by that.
Thanks for the help, jared > On Feb 23, 2017, at 5:47 PM, Timothy Coalson <[email protected]> wrote: > > wb_command -file-information has a column with a count of inf/NaN values. > > Since -fix-zeros has an effect, I suspect that some kind of thresholding is > going on in fsl_view, rather than the smoothing being the issue. > > The volume parcel smoothing will output zero values anywhere that you don't > have a parcel, so of course it will have that kind of "hole" regardless of > the options used. > > The .nii.gz file is compressed, so being 4.2G doesn't have that much relation > to its uncompressed size in memory, and there is also the memory required for > coloring information. You can use -volume-merge to pull a single frame from > the file so that you can load it in wb_view. > > Tim > > > On Thu, Feb 23, 2017 at 4:24 PM, Jared P Zimmerman <[email protected] > <mailto:[email protected]>> wrote: > 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] >> <mailto:[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 >> _______________________________________________ >> HCP-Users mailing list >> [email protected] <mailto:[email protected]> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
