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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MikeyMalina
January 12, 2021 05:21PM
Here is that code, thanks for the tip. As far as @djunct_overlap_check, my AFNI (19.0) does not seem to recognize it as a viable command. What version are you running it on? 
#!/usr/bin/env tcsh

# created by uber_subject.py: version 0.37 (April 14, 2015)
# creation date: Thu Dec 31 14:20:32 2015

# set data directories
set top_dir   = /project2/jschnei1/MRI/MJE/MJ_022_10012020
set anat_dir  = $top_dir/Nifti
set epi_dir   = $top_dir/ZShim

# set subject and group identifiers
set subj      = MJ_022_10012020
set group_id  = test

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj                                                     \
        -script proc.$subj.IGT -scr_overwrite                                   \
        -blocks despike tshift align tlrc volreg blur mask scale regress        \
        -copy_anat $top_dir/nlWarp/022_10012020_anatWarped/anatSS.022_10012020.nii                  	\
	-anat_has_skull no 							\
        -anat_follower anat_w_skull anat $anat_dir/MJ_022-S1_WIP_T1_W_3D_5_1.nii           \
        -tcat_remove_first_trs 0                                                \
        -tshift_opts_ts -tpattern altplus                                       \
        -dsets $epi_dir/MJ022+orig.HEAD                   \
        -volreg_align_to MIN_OUTLIER                                            \
        -tlrc_base $top_dir/nlWarp/MNI152_2009_template_SSW.nii.gz                              \
        -volreg_align_e2a                                                       \
        -volreg_tlrc_warp                                                       \
	-tlrc_NL_warp								\
	-tlrc_NL_warped_dsets							\
		$top_dir/nlWarp/022_10012020_anatWarped/anatQQ.022_10012020.nii			\
		$top_dir/nlWarp/022_10012020_anatWarped/anatQQ.022_10012020.aff12.1D			\
		$top_dir/nlWarp/022_10012020_anatWarped/anatQQ.022_10012020_WARP.nii			\
        -blur_size 5.0                                                          \
        -mask_epi_anat yes                                                      \
        -regress_stim_times                                                     \
            $top_dir/control.txt                                                \
            $top_dir/losses.txt                                                 \
            $top_dir/selAB.txt                                                  \
            $top_dir/selCD.txt                                                  \
            $top_dir/wins.txt                                                   \
        -regress_stim_labels                                                    \
            control losses selAB selCD wins                                     \
        -regress_basis 'GAM'                                                    \
        -regress_censor_motion 0.3                                              \
        -regress_apply_mot_types demean deriv                                   \
        -regress_motion_per_run                                                 \
        -regress_opts_3dD                                                       \
            -gltsym 'SYM: wins -losses' -glt_label 1 wins-losses                \
            -gltsym 'SYM: selAB -selCD' -glt_label 2 selAB-selCD                \
            -gltsym 'SYM: .5*selAB +.5*selCD -control' -glt_label 3 sel-control \
	-regress_reml_exec							\
        -regress_anaticor_fast                                                  \
        -regress_make_ideal_sum sum_ideal.1D                                    \
        -regress_est_blur_epits                                                 \
        -regress_est_blur_errts                                                 \
        -regress_run_clustsim no
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Subject Author Posted

Odd crash and error during afniproc.py Attachments

MikeyMalina January 12, 2021 03:43PM

Re: Odd crash and error during afniproc.py

ptaylor January 12, 2021 04:34PM

Re: Odd crash and error during afniproc.py

MikeyMalina January 12, 2021 05:21PM

Re: Odd crash and error during afniproc.py

ptaylor January 12, 2021 05:56PM

Re: Odd crash and error during afniproc.py Attachments

MikeyMalina January 19, 2021 02:33PM

Re: Odd crash and error during afniproc.py

ptaylor January 19, 2021 03:54PM

Re: Odd crash and error during afniproc.py

MikeyMalina January 19, 2021 03:56PM

Re: Odd crash and error during afniproc.py

MikeyMalina January 28, 2021 11:19AM