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

History of AFNI updates  

|
November 18, 2010 10:00AM
I'm getting a strange error that I don't know how to parse when I run afni_proc.py. The command follows; $s is a subject ID, and the stim_files are 2 columns of 1544 TRs each, with each element either a 1 or a 0, while the datasets are 8 runs of 195 TRs each (which adds up to 1544 when you subtract 2 TRs per run):

afni_proc.py \
-subj_id ${s}.blur0 \
-blocks tshift despike volreg mask scale regress tlrc \
-dsets raw_data/${s}_run?+orig.HEAD \
-tcat_remove_first_trs 2 \
-copy_anat anat/${s}_MPRAGE_r5+orig \
-regress_stim_files regressors/${s}_allruns_vsvc.1D \
-regress_stim_labels exp vc

It gets through the "scale," block, then fails on the "regress" block. Here's the trace I get from attempting this:

** warning: removing first 2 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
-- tcat: reps is now 193
-- volreg: base/sub indices are 0, 2
++ updating polort to 3, from run len 386.0 s
-- old stim list: ['stimuli/513_allruns_vsvc.1D']
++ new stim list: ['stimuli/stim_times.01.1D', 'stimuli/stim_times.02.1D']
Traceback (most recent call last):
File "/usr/csbmb/pkg/AFNI/afni/bin/afni_proc.py", line 1513, in <module>
run_proc()
File "/usr/csbmb/pkg/AFNI/afni/bin/afni_proc.py", line 1501, in run_proc
rv = ps.create_script()
File "/usr/csbmb/pkg/AFNI/afni/bin/afni_proc.py", line 997, in create_script
cmd_str = BlockCmdFunc[block.label](self, block)
File "/usr/pni/pkg/AFNI/AFNI_2010_11_14_NIH.CentOS.5.3_64/bin/db_mod.py", line 2168, in db_cmd_regress
(ind+1, proc.stims[ind], basis[ind])
IndexError: list index out of range

I have a feeling this is dead easy, but I can't figure it out. Help?
Subject Author Posted

"list index out of range" in afni_proc.py

Matt Weber November 18, 2010 10:00AM

Re: "list index out of range" in afni_proc.py

Matt Weber November 18, 2010 12:41PM

Re: "list index out of range" in afni_proc.py

rick reynolds November 18, 2010 04:02PM

Re: "list index out of range" in afni_proc.py

rick reynolds November 18, 2010 04:45PM

Re: "list index out of range" in afni_proc.py

PeterK June 20, 2015 02:16PM

Re: "list index out of range" in afni_proc.py

rick reynolds June 21, 2015 08:29AM