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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Daniel Glen
September 29, 2022 05:42PM
Hi Stefano,
Hmm, it seems you are right about this. I haven't tracked this down to where it happens inside 3dSkullstrip, but it's not too bad a workaround using the recommended code for masking the original volume that comes at the end of its terminal output:

3dcalc -a anat_oblique.nii.gz -b anat_ns_notoblique.nii.gz -expr 'a*step(b)' -prefix anat_ns_oblique.nii.gz

The obliquity will come from the original dataset. The other way to do this is to use either nifti_tool to modify the header or 3dinfo to modify the AFNI header which propagates from AFNI's IJK_TO_DICOM_REAL attribute down to the NIFTI header's sform matrix.

3drefit -atrcopy IJK_TO_DICOM_REAL original_dset modified_dset

Thanks for letting me know about this. I'll look into this some more.
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3dSkullStrip seems to change Sform and Qform of oblique datasets Attachments

smoia September 27, 2022 05:09AM

Re: 3dSkullStrip seem to change Sforma nd Qform of oblique datasets

Daniel Glen September 29, 2022 05:42PM