help > Smoothing ROIs
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Apr 24, 2015 04:04 PM | Rachel Jonas
Smoothing ROIs
Hi, I have imported some nii.gz files (which were converted from
the FreeSurfer subcortical atlas) into BNV. When I view them on a
SurfTemplate brain as ROIs, they look quite "voxel-ey". I checked
the "smooth" option, and now they look extremely rounded and
inaccurate (like they have been smoothed too much). Is there any
way to just smooth the images a little bit so they don't look like
balloons, and still look biologically accurate? I can provide
pictures if that is helpful.
May 3, 2015 02:05 AM | Mingrui Xia
RE: Smoothing ROIs
Hi, please edit the BrainNet.m in line 621~623, there are three
'vol = smooth3(vol);'. Please delete the later two for little
smoothing. Please let me know if any further problem.
Best
Mingrui
Best
Mingrui
Sep 19, 2016 10:09 PM | Ruiyang Ge
RE: Smoothing ROIs
Hey,
I have the similar question. I tried to compare and load images indicating two different parcellation results of the same region. However, with the smoothing of the ROIs, the border of the two figures are visually so different, even after deleting the two lines of "vol=smooth3(vol)"! I have attached a figure depicting this problem. Any ideas on handling this? Thanks.
Cheers,
Ruiyang
I have the similar question. I tried to compare and load images indicating two different parcellation results of the same region. However, with the smoothing of the ROIs, the border of the two figures are visually so different, even after deleting the two lines of "vol=smooth3(vol)"! I have attached a figure depicting this problem. Any ideas on handling this? Thanks.
Cheers,
Ruiyang
Sep 20, 2016 05:09 PM | Mingrui Xia
RE: Smoothing ROIs
Hi Ruiyang,
Thanks for your feedback. Could you please upload your nifti file for testing?
Best,
Mingrui
Thanks for your feedback. Could you please upload your nifti file for testing?
Best,
Mingrui
Sep 20, 2016 07:09 PM | Ruiyang Ge
RE: Smoothing ROIs
Hi,
Thanks for your writing. Please find the file.
Cheers,
Ruiyang
Thanks for your writing. Please find the file.
Cheers,
Ruiyang
Sep 21, 2016 05:09 PM | Mingrui Xia
RE: Smoothing ROIs
Hi,
Please modify the vol = smooth3(vol); to vol = smooth3(vol,'gaussian');
Using the Gaussian kernel instead of the default box kernel can solve the issue.
Best,
Mingrui
Please modify the vol = smooth3(vol); to vol = smooth3(vol,'gaussian');
Using the Gaussian kernel instead of the default box kernel can solve the issue.
Best,
Mingrui
Sep 21, 2016 05:09 PM | Ruiyang Ge
RE: Smoothing ROIs
Hey,
Thanks for your writing. It seems work well:)
Thanks for your writing. It seems work well:)