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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:
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
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
| July 18, 2019 03:47PM | |
Hi Paul-
I think much of the problem is caused by how you Z-padded the image. It looks like you were taking out slices instead of adding. My final commands to get pretty decent alignment are below. I did skull strip both anatomicals.
Edited 3 time(s). Last edit at 07/18/2019 04:02PM by Peter Molfese.
I think much of the problem is caused by how you Z-padded the image. It looks like you were taking out slices instead of adding. My final commands to get pretty decent alignment are below. I did skull strip both anatomicals.
#strip anatomical 3dSkullStrip -input anat.nii -prefix anat_ns.nii #z-pad low-res image 3dZeropad -I 20 -P 20 -A 20 -S 20 -L 20 -R 20 -prefix T1_ZP.nii t1_dyn_contrast_acq4.nii #now skull strip that low-res image 3dSkullStrip -prefix T1_ZP_ss.nii -input T1_ZP.nii #move low-res image center back 3drefit -dzorigin 20 T1_ZP_ss.nii #perform alignment with MutualInfo because of low contrast in image 3dAllineate -base anat_ns.nii -input T1_ZP_ss.nii -master anat_ns.nii -prefix spgr_al.nii \ -1Dmatrix_save spgr_to_t1_dyn.1D -cost mi -final wsinc5 -source_automask \ -autoweight -twopass -warp shift_rotate -verb -overwrite
Edited 3 time(s). Last edit at 07/18/2019 04:02PM by Peter Molfese.
