Here are the commands run:
wb_command -volume-parcel-smoothing \
${subID}_concat4_rfMRI_REST_hp2000_clean_.nii.gz \
MNI152_T1_2mm_strucseg_label.nii.gz \
4 \
${subID}_concat4_rfMRI_REST_hp2000_clean_s4Parc_0.nii.gz \
-fix-zeros
wb_command -volume-smoothing \
${subID}_concat4_rfMRI_REST_hp2000_clean_.nii.gz 4 \
${subID}_concat4_rfMRI_REST_hp2000_clean_s4.nii.gz \
-fix-zeros
I’m trying to smooth HCP volume resting-state data which I’ve demeaned and
concatenated the 4 runs. The input data doesn’t have these holes or the
dilation effect. I know you generally advise against using volume data or
doing unconstrained smoothing in the volume, but here I’m looking to compare a
normative sample from the HCP to some data we’ve collected in lab using HCP
like sequences. For mostly legacy reasons we’ve been processing this in the
volume so I’d like to work with the HCP volume data here. We will look to
using surface based methods in the future, part of my project is to do that,
but first I’d like just to look at the volume data
Thanks,
jared
> On Feb 23, 2017, at 4:07 PM, Glasser, Matthew <[email protected]> wrote:
>
> I would need more information about what you are doing to comment (i.e. what
> data is being smoothed, why, what command line was used, etc).
>
> Peace,
>
> Matt.
>
> From: <[email protected]
> <mailto:[email protected]>> on behalf of Jared P
> Zimmerman <[email protected] <mailto:[email protected]>>
> Date: Thursday, February 23, 2017 at 12:21 PM
> To: "[email protected] <mailto:[email protected]>"
> <[email protected] <mailto:[email protected]>>
> Subject: [HCP-Users] volume-smoothing and volume-parcel-smoothing introducing
> holes in data
>
> 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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> <Screen Shot 2017-02-23 at 12.53.24 PM.png><Screen Shot 2017-02-23 at 1.06.49
> PM.png>
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