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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.'
The text was updated successfully, but these errors were encountered:
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":
The text was updated successfully, but these errors were encountered: