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  

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October 17, 2016 06:22PM
Hello, I used afni_proc.py to generate a script for processing resting data. I have 4 runs of resting data. Below is the afni_proc.py command used-

afni_proc.py -subj_id 2001 -script proc.2001 -scr_overwrite \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat $Data/2001/T1.nii.gz \
-tcat_remove_first_trs 3 -dsets \
$Data/2001/Rest1.nii.gz \
$Data/2001/Rest2.nii.gz \
$Data/2001/Rest3.nii.gz \
$Data/2001/Rest4.nii.gz \
-tlrc_base MNI_avg152T1+tlrc -volreg_align_to MIN_OUTLIER \
-volreg_align_e2a -volreg_tlrc_warp -mask_segment_anat yes \
-mask_segment_erode yes -blur_size 4.0 -regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 -regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv -regress_ROI WMe \
-regress_reml_exec -regress_compute_fitts -regress_est_blur_epits \
-regress_run_clustsim no

Everything works fine until it gets to 3dTproject, and then the script crashes with this error-

++ 3dTproject: AFNI version=AFNI_16.1.10 (Apr 28 2016) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ have 4 input dataset names
++ Auto-catenated dataset has 4 runs
++ input time points = 1434 ; censored = 11 ; remaining = 1423
++ Setting up regressors
++ 4 Blocks * 1 polynomials -- 4 polort regressors
+ -- 1239 other fixed ort regressors
++ 1423 retained time points MINUS 1243 regressors ==> 180 D.O.F. left
++ no -mask option ==> processing all 2122945 voxels in dataset
++ Compute pseudo-inverse of fixed orts
++ Loading dataset

Fatal Signal 11 (SIGSEGV) received
THD_dset_censored_to_vectim
TPR_process_data
3dTproject
Bottom of Debug Stack
** Command line was:
3dTproject -polort 0 -input pb04.2001.r01.blur+tlrc. pb04.2001.r02.blur+tlrc. pb04.2001.r03.blur+tlrc. pb04.2001.r04.blur+tlrc. -censor censor_2001_combined_2.1D -cenmode ZERO -ort X.nocensor.xmat.1D -prefix test.tproject
** AFNI version = AFNI_16.1.10 Compile date = Apr 28 2016
** [[Precompiled binary linux_openmp_64: Apr 28 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=8898 bytes=18204934350
** Crash log is appended to file ...

Any suggestions on how I could fix this? I am running the script on a Linux server with 128 GB RAM and 32 cores, in case this matters. Two of the 4 runs have 358 timepoints and the other two have 359 timepoints. The file pb04...r01.blur+tlrc has a resolution of 1.5mm isotropic. TR is 0.802 seconds

Thank you
Veena
Subject Author Posted

3dTproject

vnair October 17, 2016 06:22PM

Re: 3dTproject

rick reynolds October 20, 2016 12:11PM