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 23, 2019 03:22PM
Hi, Sungjin-

That amount of obliquity shouldn't matter at all-- I would not bother with deobliquing it.

Those voxels are standard+large, so I don't think those dsets are so huge.

The script that you attached (several hundred lines of commented beauty) was generated by a single AFNI command, "afni_proc.py". If you notice, at the top of that script, it says this:
echo "auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019"
So, I wanted the command used to *generate* that script; I am noticing now that the script itself contains the afni_proc.py command used to make it, stored in a comment at the bottom (Rick Reynolds, who wrote the afni_proc.py functionality, thought of *everything*); the command was (I have removed the comment "#" symbols):
afni_proc.py -subj_id 265001 -script proc.265001 -scr_overwrite -blocks \
 tshift despike align tlrc volreg blur mask scale regress -copy_anat \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatSS.SSW.nii \
 -anat_has_skull no -dsets \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.rest1.s1+orig.HEAD \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.pv.s1+orig.HEAD \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.14p.s1+orig.HEAD \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.6p.s1+orig.HEAD \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.flk.s1+orig.HEAD \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/deob.rest2.s1+orig.HEAD \
 -tcat_remove_first_trs 0 -align_opts_aea -cost lpc+ZZ -volreg_align_to \
 MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -tlrc_base \
 MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.nii \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.aff12.1D \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW_WARP.nii \
 -blur_size 6.0 -regress_stim_times \
 /home/sungjin/fMRI/CGE/CGE_Raw_Data/Timing_CGE.txt -regress_stim_labels \
 Timing_CGE.txt -regress_basis 'BLOCK(6,1)' -regress_censor_motion 0.5 \
 -regress_apply_mot_types demean deriv -regress_motion_per_run \
 -regress_opts_3dD -jobs 4 -GOFORIT 5 -regress_reml_exec \
 -regress_compute_fitts -regress_make_ideal_sum sum_ideal.1D \
 -regress_est_blur_epits -regress_est_blur_errts

I don't see anything that particularly jumps out at me; I guess the REML part is somewhat memory intensive. I will ping Rick to see if he has any ideas on the memory aspect.

-pt
Subject Author Posted

current memory mallocated error

cooldesert October 21, 2019 02:34PM

Re: current memory mallocated error

ptaylor October 21, 2019 05:04PM

Re: current memory mallocated error

cooldesert October 23, 2019 11:57AM

Re: current memory mallocated error

ptaylor October 23, 2019 12:37PM

Re: current memory mallocated error

cooldesert October 23, 2019 12:53PM

Re: current memory mallocated error

ptaylor October 23, 2019 01:00PM

Re: current memory mallocated error Attachments

cooldesert October 23, 2019 01:41PM

Re: current memory mallocated error

ptaylor October 23, 2019 03:22PM

Re: current memory mallocated error

rick reynolds October 23, 2019 03:24PM

Re: current memory mallocated error

cooldesert October 24, 2019 01:34PM

Re: current memory mallocated error

cooldesert October 26, 2019 05:11PM

Re: current memory mallocated error

rick reynolds October 28, 2019 09:57AM

Re: current memory mallocated error

cooldesert October 31, 2019 03:29PM

Re: current memory mallocated error

rick reynolds October 31, 2019 05:08PM

Re: current memory mallocated error Attachments

cooldesert November 01, 2019 04:35PM

Re: current memory mallocated error

rick reynolds November 14, 2019 09:48AM