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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bowdensa
October 05, 2022 10:55AM
Here is the new version of the script: 
#!/bin/sh

# To run this script, use the following arguments in the specified order:
#
# argument 1 - subject ID
# argument 2 - resting state dataset
# argument 3 - anatomical dataset

afni_proc.py                                                                 \
    -subj_id                  $1                                             \
    -dsets                    $2                                             \
    -copy_anat                $3                                             \
    -blocks                   despike tshift align tlrc volreg blur mask     \
                              scale regress                                  \
    -tcat_remove_first_trs    3                                              \
    -align_opts_aea           -cost lpc+zz                                   \
                              -Allineate_opts  -source_automask+4        \
    -tlrc_base                MNI152_T1_2009c+tlrc                           \
    -tlrc_NL_warp                                                            \
    -volreg_align_e2a                                                        \
    -volreg_tlrc_warp                                                        \
    -mask_epi_anat            yes                                            \
    -blur_size                6                                              \
    -regress_anaticor                                                        \
    -regress_censor_motion    0.2                                            \
    -regress_censor_outliers  0.05                                           \
    -regress_bandpass         0.01 0.1                                       \
    -regress_apply_mot_types  demean deriv                                   \
    -regress_est_blur_epits                                                  \
    -regress_est_blur_errts


The old version doesn't have the line starting with -align_opts_aea -cost...



Edited 2 time(s). Last edit at 10/05/2022 11:42AM by ptaylor.
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Subject Author Posted

Fixing Alignment and Installing PyQt4

bowdensa October 05, 2022 09:39AM

Re: Fixing Alignment and Installing PyQt4

ptaylor October 05, 2022 09:45AM

Re: Fixing Alignment and Installing PyQt4

bowdensa October 05, 2022 10:55AM

Re: Fixing Alignment and Installing PyQt4

ptaylor October 05, 2022 11:55AM

Re: Fixing Alignment and Installing PyQt4

bowdensa October 12, 2022 10:59AM