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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MayaSa
August 10, 2022 04:02AM
Hi,
Thank you for your answer.
I am using 
@SSwarper -input $subject.$session.anat+orig.BRIK -base /Users/ramotlab/abin/MNI152_2009_template_SSW.nii.gz -subid $subject.$session.$scan.SE
and afterward the proc.py commands including anat_follower_ROI.
The problem is that I am trying to get a gray matter mask in MNI (cortex+subregions) extracted from freesurfer parcellation aparc+aseg and the transformation is not going well.
I tried:
to create the gray matter mask: 
mri_binarize --i aparc+aseg.s1.mgz --gm --o GMmask.s1.mgz

to convert the mgz file to nii: 
mri_convert GMmask.s1.mgz GMmask.s1.nii

to transform grom nii to afni format: 
3dcopy GMmask.s1.nii GMmask.s1.use

to use the transformation matrix from @SSwarper conducted for proc.py to transform the mask to MNI: 
3dNwarpApply -nwarp 'anatQQ.sub1.s1.movie1.SE_WARP.nii anatQQ.sub1.s1.movie1.SE.aff12.1D' -source GMmask.s1.use+orig

It comes out in orig and with no alignment to the anat data.
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Subject Author Posted

aparc+aseg to MNI

MayaSa August 09, 2022 08:14AM

Re: aparc+aseg to MNI

Peter Molfese August 09, 2022 09:16AM

Re: aparc+aseg to MNI

ptaylor August 09, 2022 09:24AM

Re: aparc+aseg to MNI

MayaSa August 10, 2022 04:02AM

Re: aparc+aseg to MNI

ptaylor August 10, 2022 11:49AM

Re: aparc+aseg to MNI

ptaylor August 10, 2022 12:00PM

Re: aparc+aseg to MNI

MayaSa August 11, 2022 06:16AM