Welcome! Log In Create A New Profile

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

History of AFNI updates

Previous Message Next Message

Message List New Topic Print View

maitra

April 03, 2015 04:28PM

Registered: 9 years ago
Posts: 146

I guess, my question is given the aligned functional image and the aligned anatomic image, how do I get the two image volumes aligned. My confusion stems from the fact that both these appear to be aligned to different coordinate systems.

Btw, here is the script that uber_subject.py threw out:

#!/usr/bin/env tcsh

# created by uber_subject.py: version 0.36 (April 5, 2013)
# creation date: Fri Apr  3 15:28:20 2015

# set data directories
set top_dir   = /mnt/space/Imagination
set stim_dir  = $top_dir/registered

# set subject and group identifiers
set subj      = Imag_anat2epi
set group_id  = run1

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj                                      \
        -script proc.$subj -scr_overwrite                        \
        -blocks tshift align tlrc volreg blur mask scale regress \
        -copy_anat $top_dir/MPRAGEco.nii.gz                      \
        -tcat_remove_first_trs 0                                 \
        -dsets $top_dir/Imagination.nii.gz                       \
        -align_opts_aea -giant_move                              \
        -volreg_align_to first                                   \
        -volreg_align_e2a                                        \
        -volreg_tlrc_warp                                        \
        -blur_size 4.0                                           \
        -regress_stim_times $stim_dir/stim_times.1D              \
        -regress_stim_labels                                     \
            stim_times.1D                                        \
        -regress_basis 'BLOCK(30)'                               \
        -regress_censor_motion 0.3                               \
        -regress_reml_exec                                       \
        -regress_make_ideal_sum sum_ideal.1D                     \
        -regress_est_blur_epits                                  \
        -regress_est_blur_errts

Edited 1 time(s). Last edit at 04/03/2015 04:29PM by maitra.

Reply Quote

RSS

Subject	Author	Posted
is it better to use align_epi_anat.py or use alignment within afni_proc.py?	maitra	March 31, 2015 01:43PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	rick reynolds	March 31, 2015 09:47PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	maitra	April 02, 2015 06:28PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	rick reynolds	April 02, 2015 09:17PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	maitra	April 02, 2015 11:05PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	maitra	April 03, 2015 04:28PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	Isaac Schwabacher	April 03, 2015 04:44PM
Re: is it better to use align_epi_anat.py or use alignment within afni_proc.py?	rick reynolds	April 07, 2015 08:58AM