regress ventricle signal in task based experiment without access to freesurfer

prerona · September 20, 2017, 5:29am

Hi

I am trying to follow proc.py help page example 11b
After running the command I get this message:
– no 3dClustSim(since no blur estimation)
-volreg_align_e2a: Command not found
It still created the proc.py command. I ran it twice but it hanged
Can you advise me?
I have copy pasted below the cmd.ap file
I can send the proc.py if it is helpful

I would really be grateful for any advice / suggestions!

============================================
#!/usr/bin/env tcsh

created by uber_subject.py: version 0.36 (April 5, 2013)

creation date: Tue Sep 19 14:40:11 2017

set subject and group identifiers

set subj = ZK1081
set group_id = test

set data directories

set top_dir = /nfs/mint/delgado_remove_ventricle/$subj
set stim_dir = $top_dir/stimuli

run afni_proc.py to create a single subject processing script

-volreg_align_to third

-regress_stim_times $stim_dir/ZK1081_anticip4_050615.txt \

-regress_stim_labels \

ZK1081_anticip4_050615.txt \

-regress_basis ‘GAM’ \

-regress_bandpass 0.01 0.1 \

-regress_opts_3dD \

-regress_compute_fitts \

-volreg_align_to MIN_OUTLIER \

afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks despike tshift align tlrc volreg blur mask scale regress
-copy_anat $top_dir/${subj}B.anat+orig
-tcat_remove_first_trs 0
-dsets
$top_dir/${subj}B.delg1.raw+orig.HEAD
$top_dir/${subj}B.delg2.raw+orig.HEAD
$top_dir/${subj}B.delg3.raw+orig.HEAD
$top_dir/${subj}B.delg4.raw+orig.HEAD
-align_opts_aea -cost lpc+ZZ
-tlrc_base TT_N27+tlrc
-tlrc_NL_warp
-volreg_align_to third
-volreg_align_e2a
-volreg_tlrc_warp
-volreg_warp_dxyz 2.5
-blur_size 4.0
-mask_segment_anat yes
-mask_segment_erode yes
-mask_import Tvent template_ventricle_2.5mm+tlrc
-mask_intersect Svent CSFe Tvent
-regress_motion_per_run
-regress_ROI_PC Svent 3
-regress_ROI_PC_per_run Svent
-regress_make_corr_vols WMe Svent
-regress_anaticor_fast
-test_stim_files no
-regress_global_times
-regress_stim_labels
anticipationAll anticipation_2 anticipation_4 loss number
response win
-regress_basis_multi
‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(4)’ ‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(2)’
‘BLOCK(2)’
-regress_stim_types
times times times AM2 times AM2 AM2
-regress_censor_motion 1.0
-regress_censor_outliers 0.1
-regress_apply_mot_types demean deriv
-regress_opts_3dD
-jobs 3
-regress_reml_exec
-regress_compute_fitts
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits
-regress_est_blur_errts
-regress_run_clustsim yes
-regress_make_ideal_sum sum_ideal.1D

rickr · September 20, 2017, 2:19pm

Hi Prerona,

The “Command not found” error (for the e2a option) is helpful
in that it means the prior line (-volreg_align_to third) did not have
proper line continuation. That means the afni_proc.py command
ended with ‘third’, and nothing else was even seen by afni_proc.py.

The shell then thinks volreg_align_e2a is the start of a new command,
and it says “Command not found”.

Consider running your script through “file_tool -test -infile SCRIPT.txt”,
to see if it says something useful.

Why it seems that your script might have hanged is hard to tell,
but we can save those concerns for after the AP command is
working.

rick

prerona · September 20, 2017, 7:00pm

Hi Rick

thanks so much for your quick help! I made correction & it ran, properly a bit further! But now I am getting another error that I am not sure why I am getting this (I created the template_ventricle_2.5 earlier and put it in the abin + in the folder where I am running this from). I am not sure what I am doing wrong
Please could you have a look at your convenience?

Thank you so much!

Prerona

=======================================================================================

** error: option -regress_motion_per_run follows unknown arg #43 (-mask_import)

** failed command (get_user_opts):

afni_proc.py -subj_id ZK1081 -script proc.ZK1081 -scr_overwrite -blocks
despike tshift align tlrc volreg blur mask scale regress -copy_anat
/nfs/mint/delgado_remove_ventricle/ZK1081/ZK1081B.anat+orig
-tcat_remove_first_trs 0 -dsets
/nfs/mint/delgado_remove_ventricle/ZK1081/ZK1081B.delg1.raw+orig.HEAD
/nfs/mint/delgado_remove_ventricle/ZK1081/ZK1081B.delg2.raw+orig.HEAD
/nfs/mint/delgado_remove_ventricle/ZK1081/ZK1081B.delg3.raw+orig.HEAD
/nfs/mint/delgado_remove_ventricle/ZK1081/ZK1081B.delg4.raw+orig.HEAD
-align_opts_aea -cost lpc+ZZ -tlrc_base TT_N27+tlrc -tlrc_NL_warp
-volreg_align_to third -volreg_align_e2a -volreg_tlrc_warp
-volreg_warp_dxyz 2.5 -blur_size 4.0 -mask_segment_anat yes
-mask_segment_erode yes -mask_import Tvent
template_ventricle_2.5mm+tlrc -mask_intersect Svent CSFe Tvent
-regress_motion_per_run -regress_ROI_PC Svent 3 -regress_ROI_PC_per_run
Svent -regress_make_corr_vols WMe Svent -regress_anaticor_fast
-test_stim_files no -regress_global_times -regress_stim_labels
anticipationAll anticipation_2 anticipation_4 loss number response win
-regress_basis_multi ‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(4)’ ‘BLOCK(2)’
‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(2)’ -regress_stim_types times times times
AM2 times AM2 AM2 -regress_censor_motion 1.0 -regress_censor_outliers
0.1 -regress_apply_mot_types demean deriv -regress_opts_3dD -jobs 3
-regress_reml_exec -regress_compute_fitts -regress_make_ideal_sum
sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts
-regress_run_clustsim yes -regress_make_ideal_sum sum_ideal.1D

=======================================================================================

ONCE AGAIN HERE IS MY CMD.AP file

#!/usr/bin/env tcsh

created by uber_subject.py: version 0.36 (April 5, 2013)

creation date: Tue Sep 19 14:40:11 2017

set subject and group identifiers

set subj = ZK1081
set group_id = test

set data directories

set top_dir = /nfs/mint/delgado_remove_ventricle/$subj
set stim_dir = $top_dir/stimuli

afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks despike tshift align tlrc volreg blur mask scale regress
-copy_anat $top_dir/${subj}B.anat+orig
-tcat_remove_first_trs 0
-dsets
$top_dir/${subj}B.delg1.raw+orig.HEAD
$top_dir/${subj}B.delg2.raw+orig.HEAD
$top_dir/${subj}B.delg3.raw+orig.HEAD
$top_dir/${subj}B.delg4.raw+orig.HEAD
-align_opts_aea -cost lpc+ZZ
-tlrc_base TT_N27+tlrc
-tlrc_NL_warp
-volreg_align_to third
-volreg_align_e2a
-volreg_tlrc_warp
-volreg_warp_dxyz 2.5
-blur_size 4.0
-mask_segment_anat yes
-mask_segment_erode yes
-mask_import Tvent template_ventricle_2.5mm+tlrc
-mask_intersect Svent CSFe Tvent
-regress_motion_per_run
-regress_ROI_PC Svent 3
-regress_ROI_PC_per_run Svent
-regress_make_corr_vols WMe Svent
-regress_anaticor_fast
-test_stim_files no
-regress_global_times
-regress_stim_labels
anticipationAll anticipation_2 anticipation_4 loss number
response win
-regress_basis_multi
‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(4)’ ‘BLOCK(2)’ ‘BLOCK(2)’ ‘BLOCK(2)’
‘BLOCK(2)’
-regress_stim_types
times times times AM2 times AM2 AM2
-regress_censor_motion 1.0
-regress_censor_outliers 0.1
-regress_apply_mot_types demean deriv
-regress_opts_3dD
-jobs 3
-regress_reml_exec
-regress_compute_fitts
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits
-regress_est_blur_errts
-regress_run_clustsim yes
-regress_make_ideal_sum sum_ideal.1D

rickr · September 20, 2017, 7:51pm

That suggests your version of AFNI is not current
enough to have that option. What does “afni -ver” show?

rick

prerona · September 20, 2017, 11:23pm

Hi Rick

Thank you so much! I am getting Precompiled binary linux_openmp_64: Sep 25 2015 (Version AFNI_2011_12_21_1014). Is this old one?

rickr · September 21, 2017, 10:21pm

Yes, that build data shows September, 2015.
The -mask_import option was added Oct 9, 2016,
so you’ll need to update.

rick

prerona · October 4, 2017, 5:59pm

Hi

we updated using the linux 64 bit link here https://afni.nimh.nih.gov/download (OpenMP 64-bit).
but now afni -ver gives me Precompiled binary linux_openmp_64: Jul 8 2015 (Version AFNI_17.2.16)
ami I going to the wrong location or something?

best

Prerona

rickr · October 4, 2017, 8:12pm

Hi Prerona,

You updated just a couple of hours too early…

The time stamp on that build computer was off at the
last build, and then it was down for a while and those
binaries did not get updated.

But I just finished rebuilding them with a corrected
time stamp. So try updating one more time.

rick