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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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wmckinney
June 29, 2021 11:44AM
Hi all,

I am using whereami -mask_atlas_region to save out some brainstem/cerebellum masks that are subsequently combined into a single mask for later analysis. I previously had no issues with this using AFNI v19.0.25 and using the following command after using @SUMA_Make_Spec_FS: 

@MakeLabelTable -atlasize_labeled_dset aparc.a2009s+aseg_rank.nii -replace
whereami -atlas aparc.a2009s+aseg_rank -mask_atlas_region aparc.a2009s+aseg_rank::brain-stem
whereami -atlas aparc.a2009s+aseg_rank -mask_atlas_region aparc.a2009s+aseg_rank::Cerebellum
whereami -atlas aparc.a2009s+aseg_rank -mask_atlas_region aparc.a2009s+aseg_rank::Cerebellum-WhiteMatter
whereami -atlas aparc.a2009s+aseg_rank -mask_atlas_region aparc.a2009s+aseg_rank::VentralDC

# Combine separate masks into a single mask
3dMean -prefix Cerebellum_BrainStem_Mask_{$subj} -mask_union \
	aparc.a2009s+aseg_rank.brain-stem+orig \
	aparc.a2009s+aseg_rank.Cerebellum+orig \
	aparc.a2009s+aseg_rank.Cerebellum-WhiteMatter+orig \
	aparc.a2009s+aseg_rank.VentralDC+orig

I recently updated from AFNI v19.0.25 to v21.0.03 and the atlas now separates left and right cerebellum. This is not an issue and I updated my code to reflect some of the comments in this thread. My new code is below: 

@MakeLabelTable -atlasize_labeled_dset aparc.a2009s+aseg.nii -replace
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Brain-Stem
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Left-Cerebellum-Cortex
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Right-Cerebellum-Cortex
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Left-Cerebellum-White-Matter
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Right-Cerebellum-White-Matter
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Left-VentralDC
whereami -atlas aparc.a2009s+aseg -mask_atlas_region aparc.a2009s+aseg::Right-VentralDC

# Combine separate masks into a single mask
3dMean -prefix Cerebellum_BrainStem_Mask_{$subj} -mask_union \
	aparc.a2009s+aseg.Brain-Stem+orig \
	aparc.a2009s+aseg.Left-Cerebellum-Cortex.l+orig \
	aparc.a2009s+aseg.Right-Cerebellum-Cortex.r+orig \
	aparc.a2009s+aseg.Left-Cerebellum-White-Matter.l+orig \
	aparc.a2009s+aseg.Right-Cerebellum-White-Matter.r+orig \
	aparc.a2009s+aseg.Left-VentralDC.l+orig \
	aparc.a2009s+aseg.Right-VentralDC.r+orig

There now is consistently a gap in my mask in medial cerebellum, however. See attached images of the union mask created by 3dMean with an overlay showing disparities between what I think is being called from the overlaid aparc.a2009s+aseg dataset and my new underlay mask. There seems to be portions of medial cerebellum included in the atlas overlay that are not being included in my whereami call and I'm not sure why this is happening. I feel like I'm missing something obvious but am at a loss?

-Walker
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Attachments:
open | download - Underlay only.PNG (98.8 KB)
open | download - overlay and underlay.PNG (105.7 KB)
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Subject Author Posted

whereami aparc medial cerebellum deletion Attachments

wmckinney June 29, 2021 11:44AM

Re: whereami aparc medial cerebellum deletion

ptaylor June 29, 2021 02:16PM

Re: whereami aparc medial cerebellum deletion

wmckinney July 05, 2021 07:11PM