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  

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Tim
December 07, 2009 12:17PM
I use the following command to generate the script for analysis of our dataset.

afni_proc.py -subj_id s1sm.align \
-dsets Data/s1sm?+orig.HEAD \
-blocks volreg blur mask scale regress \
-do_block align tlrc \
-copy_anat Data/s1_t2+orig \
-tcat_remove_first_trs 2 \
-volreg_align_to last \
-volreg_align_e2a \
-volreg_tlrc_warp \
-tlrc_base TT_EPI+tlrc \
-regress_stim_times stimes.sm.1D \
-regress_stim_labels SM \
-regress_basis 'BLOCK(15,1)' \
-regress_censor_motion 1.0 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-remove_preproc_files \
-execute

However, once I look at the statistics I get activation all over the place, even outside the brain (see attached screenshot). Did I miss any step in the script? Or are there any steps I need to take after running the analysis? I could also submit the origninal dataset, if you want to take a look at it.

Thanks for your help,

Tim
Subject Author Posted

Stats outside the brain

Tim December 07, 2009 12:17PM

Re: Stats outside the brain

Tim December 07, 2009 12:18PM

Re: Stats outside the brain

rick reynolds December 07, 2009 12:29PM

Re: Stats outside the brain

Tim December 07, 2009 01:05PM

Re: Stats outside the brain

rick reynolds December 07, 2009 01:08PM