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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Sabrina
October 19, 2015 11:10AM
I used the following commands before using masks based on the TT_Daemon standard.
Thank you!

$ to3d -time:zt 36 163 2000 alt+z2 *.IMA
$ afni_proc.py -subj_id NI12_SMc -dsets run1+orig run2+orig run3+orig run4+orig -blocks tshift volreg blur mask scale regress -copy_anat anat+orig -do_block align tlrc -volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_in_automask -regress_stim_times stimes.NT1.1D stimes.NT2.1D stimes.NT3.1D stimes.ND1.1D stimes.ND2.1D stimes.ND3.1D stimes.ST1.1D stimes.ST2.1D stimes.ST3.1D stimes.SD1.1D stimes.SD2.1D stimes.SD3.1D stimes.SAM.1D -test_stim_files no -regress_stim_labels NT1 NT2 NT3 ND1 ND2 ND3 ST1 ST2 ST3 SD1 SD2 SD3 SAM -regress_basis 'TENT(0,16,9)' -regress_opts_3dD -num_glt 16 -GOFORIT 13 -allzero_ok -gltsym 'SYM: +NT1 +NT2 +NT3 -ND1 -ND2 -ND3' -glt_label 1 NTvND -gltsym 'SYM: +ST1 +ST2 +ST3 -SD1 -SD2 -SD3' -glt_label 2 STvSD -gltsym 'SYM: +NT1 +NT2 +NT3 -ST1 -ST2 -ST3' -glt_label 3 NTvST -gltsym 'SYM: +ND1 +ND2 +ND3 -SD1 -SD2 -SD3' -glt_label 4 NDvSD -gltsym 'SYM: +NT1 -NT2 -NT3' -glt_label 5 NTrep -gltsym 'SYM: +ND1 -ND2 -ND3' -glt_label 6 NDrep -gltsym 'SYM: +ST1 -ST2 -ST3' -glt_label 7 STrep -gltsym 'SYM: +SD1 -SD2 -SD3' -glt_label 8 SDrep -gltsym 'SYM: +NT1 +ST1 -NT2 -NT3 -ST2 -ST3' -glt_label 9 Trep -gltsym 'SYM: +ND1 +SD1 -ND2 -ND3 -SD2 -SD3' -glt_label 10 Drep -gltsym 'SYM: +ST1 +SD1 -ST2 -ST3 -SD2 -SD3' -glt_label 11 Srep -gltsym 'SYM: +NT1 +ND1 -NT2 -NT3 -ND2 -ND3' -glt_label 12 Nrep -gltsym 'SYM: +NT1 +ND1 +ST1 +SD1 -NT2 -NT3 -ND2 -ND3 -ST2 -ST3 -SD2 -SD3' -glt_label 13 Rep -gltsym 'SYM: +NT1 +NT2 +NT3 +ST1 +ST2 +ST3 -ND1 -ND2 -ND3 -SD1 -SD2 -SD3' -glt_label 14 TvD -gltsym 'SYM: +ST1 +ST2 +ST3 +SD1 +SD2 +SD3 -NT1 -NT2 -NT3 -ND1 -ND2 -ND3' -glt_label 15 SvN -gltsym 'SYM: +SAM -NT1 -NT2 -NT3 -ND1 -ND2 -ND3 -ST1 -ST2 -ST3 -SD1 -SD2 -SD3' -glt_label 16 SAMvAll -regress_est_blur_epits -regress_est_blur_errts
$ tcsh -xef proc.NI12_SMc |& tee output.proc.NI12_SMc
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Subject Author Posted

correcting non-match overlay

Sabrina October 19, 2015 10:30AM

Re: correcting non-match overlay

Daniel Glen October 19, 2015 10:57AM

Re: correcting non-match overlay

Sabrina October 19, 2015 11:10AM

Re: correcting non-match overlay

Daniel Glen October 19, 2015 11:37AM

Re: correcting non-match overlay

Sabrina October 19, 2015 02:16PM

Re: correcting non-match overlay

Sabrina October 19, 2015 03:21PM

Re: correcting non-match overlay

Daniel Glen October 20, 2015 01:45PM

Re: correcting non-match overlay

Sabrina October 20, 2015 02:06PM

Re: correcting non-match overlay

Daniel Glen October 20, 2015 03:49PM