Hi, I’m new with AFNI software. I just used uber_subject.py GUI to do fMRI analysis. But now, I have new regressors so I want to use these new regressors to do the anlysis again. However, I do not want to run the whole proc.Subject again because it takes too much time. Does anybody know how to do GLM again with the new regressors without having to run all the code? Thanks.
There should be an afni_proc.py command script in the subject directory.
Copy it and add options like -write_3dD_script and -write_3dD_prefix,
which should allow you to create updated a 3dDeconvolve script.
Running the updated afni_proc.py command with those options, plus
the ones that include your new regressors, should work out.
Thanks for your response. What do you mean add options like -write_3dD_script and -write_3dD_prefix? Do you mean I should copy the ‘proc.Subject’ command to a new folder and change the regressors and then just add '-write_3dD_script ’ and ‘-write_3dD_prefix’ these two command inside the ‘proc.Subject’ command? Thanks.
Those are afni_proc.py options. Add them to your modified
afni_proc.py command script (not the proc script), and it will
generated scripts to run a modified 3dDeconvolve command.
Do you mean add the two command ‘-write_3dD_script’ and ‘-wtite_3dD_prefi’ into the ‘cmd.ap.Subj’ command script? In what position should I put these two commands? And after I place these two commands and add the new regressors, is it correct to rerun the script ‘cmd.ap.Subj’ like this: ‘tcsh -xef cmd.ap.Subj’ ?
I just re-run the ‘cmd.ap.Subj’ script like this: ’ tcsh -xef cmd.ap.Subj’. But there showed some errors saying that the ‘-write_3dD_script’ does not exis. Do you know how to solve this problem?
If it says “command not found”, then you need to fix the \ characters for line continuation. Can you post the exact error message, possibly along with your command.
set top_dir = /data/ffang3/fMRI_analysis/Subj16_guo_kai
set anat_dir = $top_dir/Raw_Data
set epi_dir = $top_dir/Raw_Data
set stim_dir = $top_dir/Time
set subj = Subject16_GuoKai
set group_id = EmotionRegulationStudy
-script proc.$subj -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale regress
gEmoReg gative utral testing
-regress_apply_mot_types demean deriv
-gltsym ‘SYM: gEmoReg -gative’ -glt_label 1 gEmoReg-gative
-gltsym ‘SYM: gEmoReg -utral’ -glt_label 2 gEmoReg-utral
-gltsym ‘SYM: gative -utral’ -glt_label 3 gative-utral
-gltsym ‘SYM: 0.333gEmoReg +0.333gative +0.333utral’
-glt_label 4 mean.GGU
-gltsym 'SYM: gEmoReg -0.5gative -0.5*utral’ -glt_label 5 G-GU
I have posted my command script. Is there anything wrong with it?
The error is: ‘-write_3dD_script: Common not found’
This is missing line continuation on the first line, which
is why it is viewing -write_3dD_script as a command,
which is then not found.
Note that each of those -write_3dD_* options takes one
parameter, the script name and the desired prefix,