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

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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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January 24, 2018 04:31PM
Thanks Taylor!

Here is my afni_proc.py command.

afni_proc.py -subj_id $subj                                                  \
        -script proc.$subj -scr_overwrite                                 \
        -blocks tshift align tlrc volreg blur mask scale regress             \
        -copy_anat $anat_dir/t1_mprage+orig                      \
        -anat_has_skull no													 \
        -tcat_remove_first_trs 0                                             \
        -dsets                                                               \
            $epi_dir/DiCo_all+orig.HEAD                   \
        -volreg_align_to third                                               \
        -volreg_align_e2a                                                    \
        -volreg_tlrc_warp                                                    \
        -blur_size 4.0                                                       \
        -regress_stim_times                                                  \
            $stim_dir/Int_High.txt                                        \
            $stim_dir/Int_Low.txt                                        \
            $stim_dir/FT.txt                                        \
        -regress_stim_labels                                                 \
            Int_High Int_Low FT    \
        -regress_basis 'BLOCK(9,1)'                                      \
        -regress_censor_motion 0.3                                           \
        -regress_opts_3dD                                                    \
        	-fout -tout -bout												 \
        -regress_make_ideal_sum sum_ideal.1D                                 \
        -regress_est_blur_epits                                              \
        -regress_est_blur_errts

If you suggest me not concatenate the data before feeding it into afni_proc.py, then I have another question...As you can see from my afni_proc.py script, DiCo_all+orig is the dataset that I concatenated 3 functional data. If I put 3 functional data separately (e.g. DiCo_1, DiCo_2, and DiCo_3), how can I generate the stimulus time file? Each of stimulus time file need to put 3 rows of timing info but I only need to put the timing info in one row since each functional data only has one stimulus condition...For example, if I generate the stimulus time file for Int_High, it will be something like this.

12 42 72 102 132 162 192 222 252 282
0
0

But I believe I cannot generate the timing file in this way...and if I have only one single row, this script file cannot run properly. Any suggestions..?

Thanks!
Taek
Subject Author Posted

Best way to analyze the data Attachments

Hyuntaek January 23, 2018 02:21PM

Re: Best way to analyze the data

Peter Molfese January 23, 2018 04:39PM

Re: Best way to analyze the data

Hyuntaek January 24, 2018 04:31PM

Re: Best way to analyze the data

Peter Molfese January 25, 2018 11:47AM

Re: Best way to analyze the data

rick reynolds January 25, 2018 03:20PM

Re: Best way to analyze the data

Hyuntaek January 26, 2018 11:24AM