AFNI Message Board

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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dowdlelt
December 06, 2018 01:24PM
Hi AFNI gurus,

Hitting an issue with afni proc, attempting to use a specific mask for BlurInMask, with the following line:

-blur_in_mask yes -blur_opts_BIM -mask ~/afni_global_dsets/subcortical_MNI152_2009_mask.nii \

But afni proc runs into a fatal error:

3dBlurInMask -preserve -FWHM 6 -Mmask mask_epi_anat.GM1008_subcort_ses-one+tlrc -prefix pb05.GM1008_subcort_ses-one.r01.blur -mask /home/dowdlelt/afni_global_dsets/subcortical_MNI152_2009_mask.nii pb04.GM1008_subcort_ses-one.r01.volreg+tlrc
++ 3dBlurInMask: AFNI version=AFNI_18.3.09 (Nov 27 2018) [64-bit]
++ Authored by: RW Cox
++ 1 unique nonzero values in -Mmask; 66579 nonzero voxels
** FATAL ERROR: Can't have two mask inputs

I am doing this to limit blurring to subcortical structures, as I am doing cortical analyses with the surface pipeline and don't want to blur in insula for example. Is there an option I am missing or perhaps specifying wrong? Thank you, as always.
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Blur_in_mask issue, can't use specific mask?

dowdlelt December 06, 2018 01:24PM