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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jvaidya
January 12, 2016 01:40PM
Hi,

I've been trying for sometime to implement 3dQwarp and 3dNwarpApply. Qwarp seems to work great but I can't get my EPI image to line-up with the template. Here's an example script. I did check that the EPI got coregistered properly with align_epi_ant.py. I also checked that the t1 got registered to the TT_N27 template. I'm guessing that I'm doing something wrong with "-nwarp" but I can't seem to figure out what that it is (or perhaps some other options are necessary). Thank you for your help!

Jatin

3dUnifize -prefix t1h_U -input t1h.nii
3dSkullStrip -input t1h_U+orig -prefix t1h_US -niter 400 -ld 40
3dAllineate -prefix t1h_USA -base /opt/afni/TT_N27+tlrc \
-source t1h_US+orig -twopass -cost lpa \
-1Dmatrix_save t1h_USA.aff12.1D \
-autoweight -fineblur 3 -cmass

3dQwarp -prefix t1hQw -duplo -useweight -blur 0 3 -base /opt/afni/TT_N27+tlrc -source t1h_USA+tlrc

align_epi_anat.py -anat t1h_U+orig -epi A-19_zpad.nii \
-epi_base 3 -epi2anat -ginormous_move

3dNwarpApply -prefix A-19_zpad_QW+tlrc -source A-19_zpad.nii \
-nwarp 't1hQw_WARP+tlrc t1h_USA.aff12.1D
A-19_zpad_al_reg_mat.aff12.1D'
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Subject Author Posted

NWarpApply

jvaidya January 12, 2016 01:40PM

Re: NWarpApply

jkeidel January 12, 2016 01:47PM

Re: NWarpApply

Daniel Glen January 12, 2016 03:41PM

Re: NWarpApply

jvaidya January 12, 2016 03:42PM

Re: NWarpApply

jvaidya January 14, 2016 12:24PM