Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cleanup option from SPM -> remove? #5

Open
ChristophePhillips opened this issue Jun 10, 2016 · 0 comments
Open

Cleanup option from SPM -> remove? #5

ChristophePhillips opened this issue Jun 10, 2016 · 0 comments
Assignees
Labels

Comments

@ChristophePhillips
Copy link
Member

ChristophePhillips commented Jun 10, 2016

When requesting a 'clean up' at the end of the segmentation, it uses standard SPM code: SPM's code relies firstly on WM map and start with some erosion steps... Then it uses GM and WM for some conditional dilation, then it's used to clean up GM/WM region. Further there is some CSF cleaning. [*]
Trouble is with a lesion we've got an extra tissue class between WM and CSF. Then SPM will assume that 'lesion' is the CSF!
-> the clean up option should probably be removed as it may not work as expected?

[*] see subfunction "clean_gwc" in "spm_preproc_write8.m" and the help inside the cfg routine "spm_cfg_preproc8.m":

'This uses a crude routine for extracting the brain from segmented images. It begins by taking the white matter, and eroding it a couple of times to get rid of any odd voxels. The algorithm continues on to do conditional dilations for several iterations, where the condition is based upon gray or white matter being present.This identified region is then used to clean up the grey and white matter partitions. Note that the fluid class will also be cleaned, such that aqueous and vitreous humour in the eyeballs, as well as other assorted fluid regions (except CSF) will be removed.'
'If you find pieces of brain being chopped out in your data, then you may wish to disable or tone down the cleanup procedure. Note that the procedure uses a number of assumptions about what each tissue class refers to. If a different set of tissue priors are used, then this routine should be disabled.'

@ChristophePhillips ChristophePhillips self-assigned this Jun 10, 2016
ChristophePhillips added a commit that referenced this issue Oct 26, 2017
Adding the "subcortex wo BG" (#5) and "BG only" (#6) masks
Fixing small error in other mak generation.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant