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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sungshinkim
August 26, 2016 10:53AM
Hello,

Could you please help to alignment between anatomical image and functional images?
There is significant misalignment between the two.
Here is the script using afni_proc.py..


#!/bin/tcsh -xef
set work_dir = /Volumes/fsmresfiles/MSS/Voss_Lab/DERVISH/Backup
set subj = subj01
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale \
-copy_anat $work_dir/$subj/epi_$subj.anat+orig \
-tlrc_base TT_avg152T1+tlrc \
-tcat_remove_first_trs 0 \
-dsets $work_dir/$subj/epi_$subj.r0*+orig.HEAD \
-volreg_align_to third \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_opts_vr -twopass \
-align_opts_aea -cost lpc+ZZ -giant_move \
-volreg_zpad 4 \
-blur_size 4.0



I tried several options with different cost function, maybe I might need to try uber_align_test.py
Also, I would like to send the files to check.


Sincerely,
Sungshin Kim
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Subject Author Posted

Poor alignment, please help

sungshinkim August 26, 2016 10:53AM

Re: Poor alignment, please help

Daniel Glen August 26, 2016 02:45PM

Re: Poor alignment, please help

Daniel Glen September 09, 2016 02:56PM