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

@SSwarper -input C1051_SurfVol.nii.gz -base MNI152_2009_template_SSW.nii.gz -subid Subj01 -skipwarp
3dZeropad -I 20 -P 20 -A 5 -prefix epi1_rs.nii.gz epi_mean_test.nii.gz 

#Align anat to EPI
 3dAllineate \
 -base  epi1_rs.nii.gz \
 -input anatSS.Subj01.nii \
 -prefix tmp.anat.aligned.nii.gz \
 -1Dmatrix_save epi1_rs_al_12.1D \
 -cost lpc \
 -final wsinc5 \
 -source_automask -autoweight \
 -twopass \
 -verb

#invert transform
cat_matvec epi1_rs_al_12.1D -I > epi2anat_12.1D

#apply inverted transform
3dAllineate -base C1051_SurfVol.nii.gz -input epi1_rs.nii.gz -1Dmatrix_apply epi2anat_12.1D -prefix epi_aligned.nii.gz