open-discussion
open-discussion > RE: brain masking, skull striping
Dec 11, 2019 04:12 PM | gpicci - The Pennsylvania State University
RE: brain masking, skull striping
Hi Martin,
I am also having a similar issue. The rest of DTIprep runs smoothly, but I keep getting brains that are not properly skull stripped. I am getting the following error message:
Brain Mask
Brain Mask FSL
/Path/To/ImageMath
ImageMath cannot be started.
Any ideas what issue this may be? Also, you mention that the ImageMath folder has to be before the paths of other tools - what do you mean by this? Does ImageMath need to be a directory above other tools?
Thank you for your help!
Giorgia
Originally posted by Martin Styner:
I am also having a similar issue. The rest of DTIprep runs smoothly, but I keep getting brains that are not properly skull stripped. I am getting the following error message:
Brain Mask
Brain Mask FSL
/Path/To/ImageMath
ImageMath cannot be started.
Any ideas what issue this may be? Also, you mention that the ImageMath folder has to be before the paths of other tools - what do you mean by this? Does ImageMath need to be a directory above other tools?
Thank you for your help!
Giorgia
Originally posted by Martin Styner:
The Slicer brain masking is not the best (which
is likely why there's still skull in the image,I assume that
something was removed?). For the FSL option, our tool ImageMath is
used. Unfortunately there are other tools that have also an
ImageMath binary (e.g. ANTs or Rview), so you need to make sure
that the path to DTIPrep's ImageMath folder has to be before the
paths of the other tools.
I usually use bet with IDWI
Martin
I usually use bet with IDWI
Martin
Threaded View
| Title | Author | Date |
|---|---|---|
| Daniel Berge | Jan 4, 2018 | |
| Martin Styner | Jan 5, 2018 | |
| gpicci | Dec 11, 2019 | |
| Yingying Wang | Mar 4, 2022 | |
| Martin Styner | Mar 4, 2022 | |
| Daniel Berge | Jan 18, 2018 | |