3dANOVA3 buffer overflow detected

AFNI Message Board
1

Dear AFNI experts,

I have used 3dANOVA3 to run the statistics on my data. However, I have encountered the following crash. The crash log cannot be attached but if you need I can send through email.
I have used 3dANOVA3 before, and it didn’t have such crash. Considering if it is out of RAM (Since another script is running taking up 97% memory), I also tested the previous scripts and it still worked. I have no idea how this crash come.
Can you please kindly suggest how to solve it?

%%%%%%%%%%%%%%%%%%%
++ 3dANOVA3: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: B. Douglas Ward
++ Mask from dataset ‘/media/raymondlab/Xin/tDCS/post_analy/brain_msk_2mm.nii’ has 233961 voxels
Data set dimensions: nx = 91 ny = 109 nz = 91 nxyz = 902629
Number of input datasets = 120
*** buffer overflow detected ***: 3dANOVA3 terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f61c1cf37e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f61c1d9515c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7f61c1d93160]
/lib/x86_64-linux-gnu/libc.so.6(+0x1166c9)[0x7f61c1d926c9]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7f61c1cf76b0]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x139b)[0x7f61c1cca50b]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f61c1d92754]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f61c1d926ad]
3dANOVA3[0x407725]
3dANOVA3[0x4106a6]
3dANOVA3[0x417c6d]
3dANOVA3[0x406640]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f61c1c9c830]
3dANOVA3[0x4067b9]
======= Memory map: ========
00400000-0091a000 r-xp 00000000 08:07 8151383 /home/raymondlab/abin/3dANOVA3
00b1a000-00b1d000 r–p 0051a000 08:07 8151383 /home/raymondlab/abin/3dANOVA3
00b1d000-00b5d000 rw-p 0051d000 08:07 8151383 /home/raymondlab/abin/3dANOVA3
00b5d000-00bbf000 rw-p 00000000 00:00 0
00be4000-0780a000 rw-p 00000000 00:00 0 [heap]
7f61beea0000-7f61beeb7000 r-xp 00000000 08:07 2490543 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f61beeb7000-7f61bf0b6000 —p 00017000 08:07 2490543 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f61bf0b6000-7f61bf0b7000 r–p 00016000 08:07 2490543 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f61bf0b7000-7f61bf0b8000 rw-p 00017000 08:07 2490543 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f61bf0b8000-7f61c0aeb000 rw-p 00000000 00:00 0
7f61c0aeb000-7f61c0af0000 r-xp 00000000 08:07 5906445 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f61c0af0000-7f61c0cef000 —p 00005000 08:07 5906445 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f61c0cef000-7f61c0cf0000 r–p 00004000 08:07 5906445 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f61c0cf0000-7f61c0cf1000 rw-p 00005000 08:07 5906445 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f61c0cf1000-7f61c0cf3000 r-xp 00000000 08:07 5906434 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f61c0cf3000-7f61c0ef3000 —p 00002000 08:07 5906434 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f61c0ef3000-7f61c0ef4000 r–p 00002000 08:07 5906434 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f61c0ef4000-7f61c0ef5000 rw-p 00003000 08:07 5906434 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f61c0ef5000-7f61c0ef8000 r-xp 00000000 08:07 2490599 /lib/x86_64-linux-gnu/libdl-2.23.so
7f61c0ef8000-7f61c10f7000 —p 00003000 08:07 2490599 /lib/x86_64-linux-gnu/libdl-2.23.so
7f61c10f7000-7f61c10f8000 r–p 00002000 08:07 2490599 /lib/x86_64-linux-gnu/libdl-2.23.so
7f61c10f8000-7f61c10f9000 rw-p 00003000 08:07 2490599 /lib/x86_64-linux-gnu/libdl-2.23.so
7f61c10f9000-7f61c111a000 r-xp 00000000 08:07 5907812 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f61c111a000-7f61c1319000 —p 00021000 08:07 5907812 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f61c1319000-7f61c131a000 r–p 00020000 08:07 5907812 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f61c131a000-7f61c131b000 rw-p 00021000 08:07 5907812 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f61c131b000-7f61c131f000 r-xp 00000000 08:07 2490594 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f61c131f000-7f61c151e000 —p 00004000 08:07 2490594 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f61c151e000-7f61c151f000 r–p 00003000 08:07 2490594 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f61c151f000-7f61c1520000 rw-p 00004000 08:07 2490594 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f61c1520000-7f61c1655000 r-xp 00000000 08:07 5905204 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f61c1655000-7f61c1855000 —p 00135000 08:07 5905204 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f61c1855000-7f61c1856000 r–p 00135000 08:07 5905204 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f61c1856000-7f61c185a000 rw-p 00136000 08:07 5905204 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f61c185a000-7f61c1870000 r-xp 00000000 08:07 5906300 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61c1870000-7f61c1a6f000 —p 00016000 08:07 5906300 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61c1a6f000-7f61c1a70000 r–p 00015000 08:07 5906300 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61c1a70000-7f61c1a71000 rw-p 00016000 08:07 5906300 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61c1a71000-7f61c1a74000 rw-p 00000000 00:00 0
7f61c1a74000-7f61c1a7b000 r-xp 00000000 08:07 5906420 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61c1a7b000-7f61c1c7a000 —p 00007000 08:07 5906420 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61c1c7a000-7f61c1c7b000 r–p 00006000 08:07 5906420 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61c1c7b000-7f61c1c7c000 rw-p 00007000 08:07 5906420 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61c1c7c000-7f61c1e3c000 r-xp 00000000 08:07 2494966 /lib/x86_64-linux-gnu/libc-2.23.so
7f61c1e3c000-7f61c203c000 —p 001c0000 08:07 2494966 /lib/x86_64-linux-gnu/libc-2.23.so
7f61c203c000-7f61c2040000 r–p 001c0000 08:07 2494966 /lib/x86_64-linux-gnu/libc-2.23.so
7f61c2040000-7f61c2042000 rw-p 001c4000 08:07 2494966 /lib/x86_64-linux-gnu/libc-2.23.so
7f61c2042000-7f61c2046000 rw-p 00000000 00:00 0
7f61c2046000-7f61c214e000 r-xp 00000000 08:07 2494991 /lib/x86_64-linux-gnu/libm-2.23.so
7f61c214e000-7f61c234d000 —p 00108000 08:07 2494991 /lib/x86_64-linux-gnu/libm-2.23.so
7f61c234d000-7f61c234e000 r–p 00107000 08:07 2494991 /lib/x86_64-linux-gnu/libm-2.23.so
7f61c234e000-7f61c234f000 rw-p 00108000 08:07 2494991 /lib/x86_64-linux-gnu/libm-2.23.so
7f61c234f000-7f61c2375000 r-xp 00000000 08:07 2490732 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f61c2375000-7f61c2575000 —p 00026000 08:07 2490732 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f61c2575000-7f61c2577000 r–p 00026000 08:07 2490732 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f61c2577000-7f61c2578000 rw-p 00028000 08:07 2490732 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f61c2578000-7f61c2591000 r-xp 00000000 08:07 2494849 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f61c2591000-7f61c2790000 —p 00019000 08:07 2494849 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f61c2790000-7f61c2791000 r–p 00018000 08:07 2494849 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f61c2791000-7f61c2792000 rw-p 00019000 08:07 2494849 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f61c2792000-7f61c27f4000 r-xp 00000000 08:07 5906471 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f61c27f4000-7f61c29f4000 —p 00062000 08:07 5906471 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f61c29f4000-7f61c29f5000 r–p 00062000 08:07 5906471 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f61c29f5000-7f61c29fa000 rw-p 00063000 08:07 5906471 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f61c29fa000-7f61c29fb000 rw-p 00000000 00:00 0
7f61c29fb000-7f61c2a21000 r-xp 00000000 08:07 2490705 /lib/x86_64-linux-gnu/ld-2.23.so
7f61c2be5000-7f61c2bed000 rw-p 00000000 00:00 0
7f61c2c1f000-7f61c2c20000 rw-p 00000000 00:00 0
7f61c2c20000-7f61c2c21000 r–p 00025000 08:07 2490705 /lib/x86_64-linux-gnu/ld-2.23.so
7f61c2c21000-7f61c2c22000 rw-p 00026000 08:07 2490705 /lib/x86_64-linux-gnu/ld-2.23.so
7f61c2c22000-7f61c2c23000 rw-p 00000000 00:00 0
7fffe37b3000-7fffe37d8000 rw-p 00000000 00:00 0 [stack]
7fffe37f1000-7fffe37f4000 r–p 00000000 00:00 0 [vvar]
7fffe37f4000-7fffe37f6000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

Fatal Signal 6 (SIGABRT) received
3dANOVA3 main

%%%%%%%%%%%%%%%%%%%%%%%%

The script is as follows:

3dANOVA3 -type 5
-alevels 2
-blevels 5
-clevels 12
-mask $mask_dir
-dset 1 1 1 ${FC_dir}/$network/sFC_subj1_pre.nii
-dset 1 2 1 ${FC_dir}/$network/sFC_subj1_in1.nii
-dset 1 3 1 ${FC_dir}/$network/sFC_subj1_in2.nii
-dset 1 4 1 ${FC_dir}/$network/sFC_subj1_in3.nii
-dset 1 5 1 ${FC_dir}/$network/sFC_subj1_post.nii
-dset 1 1 2 ${FC_dir}/$network/sFC_subj2_pre.nii
-dset 1 2 2 ${FC_dir}/$network/sFC_subj2_in1.nii
-dset 1 3 2 ${FC_dir}/$network/sFC_subj2_in2.nii
-dset 1 4 2 ${FC_dir}/$network/sFC_subj2_in3.nii
-dset 1 5 2 ${FC_dir}/$network/sFC_subj2_post.nii
-dset 1 1 3 ${FC_dir}/$network/sFC_subj3_pre.nii
-dset 1 2 3 ${FC_dir}/$network/sFC_subj3_in1.nii
-dset 1 3 3 ${FC_dir}/$network/sFC_subj3_in2.nii
-dset 1 4 3 ${FC_dir}/$network/sFC_subj3_in3.nii
-dset 1 5 3 ${FC_dir}/$network/sFC_subj3_post.nii
-dset 1 1 4 ${FC_dir}/$network/sFC_subj4_pre.nii
-dset 1 2 4 ${FC_dir}/$network/sFC_subj4_in1.nii
-dset 1 3 4 ${FC_dir}/$network/sFC_subj4_in2.nii
-dset 1 4 4 ${FC_dir}/$network/sFC_subj4_in3.nii
-dset 1 5 4 ${FC_dir}/$network/sFC_subj4_post.nii
-dset 1 1 5 ${FC_dir}/$network/sFC_subj5_pre.nii
-dset 1 2 5 ${FC_dir}/$network/sFC_subj5_in1.nii
-dset 1 3 5 ${FC_dir}/$network/sFC_subj5_in2.nii
-dset 1 4 5 ${FC_dir}/$network/sFC_subj5_in3.nii
-dset 1 5 5 ${FC_dir}/$network/sFC_subj5_post.nii
-dset 1 1 6 ${FC_dir}/$network/sFC_subj6_pre.nii
-dset 1 2 6 ${FC_dir}/$network/sFC_subj6_in1.nii
-dset 1 3 6 ${FC_dir}/$network/sFC_subj6_in2.nii
-dset 1 4 6 ${FC_dir}/$network/sFC_subj6_in3.nii
-dset 1 5 6 ${FC_dir}/$network/sFC_subj6_post.nii
-dset 1 1 7 ${FC_dir}/$network/sFC_subj7_pre.nii
-dset 1 2 7 ${FC_dir}/$network/sFC_subj7_in1.nii
-dset 1 3 7 ${FC_dir}/$network/sFC_subj7_in2.nii
-dset 1 4 7 ${FC_dir}/$network/sFC_subj7_in3.nii
-dset 1 5 7 ${FC_dir}/$network/sFC_subj7_post.nii
-dset 1 1 8 ${FC_dir}/$network/sFC_subj8_pre.nii
-dset 1 2 8 ${FC_dir}/$network/sFC_subj8_in1.nii
-dset 1 3 8 ${FC_dir}/$network/sFC_subj8_in2.nii
-dset 1 4 8 ${FC_dir}/$network/sFC_subj8_in3.nii
-dset 1 5 8 ${FC_dir}/$network/sFC_subj8_post.nii
-dset 1 1 9 ${FC_dir}/$network/sFC_subj9_pre.nii
-dset 1 2 9 ${FC_dir}/$network/sFC_subj9_in1.nii
-dset 1 3 9 ${FC_dir}/$network/sFC_subj9_in2.nii
-dset 1 4 9 ${FC_dir}/$network/sFC_subj9_in3.nii
-dset 1 5 9 ${FC_dir}/$network/sFC_subj9_post.nii
-dset 1 1 10 ${FC_dir}/$network/sFC_subj10_pre.nii
-dset 1 2 10 ${FC_dir}/$network/sFC_subj10_in1.nii
-dset 1 3 10 ${FC_dir}/$network/sFC_subj10_in2.nii
-dset 1 4 10 ${FC_dir}/$network/sFC_subj10_in3.nii
-dset 1 5 10 ${FC_dir}/$network/sFC_subj10_post.nii
-dset 1 1 11 ${FC_dir}/$network/sFC_subj11_pre.nii
-dset 1 2 11 ${FC_dir}/$network/sFC_subj11_in1.nii
-dset 1 3 11 ${FC_dir}/$network/sFC_subj11_in2.nii
-dset 1 4 11 ${FC_dir}/$network/sFC_subj11_in3.nii
-dset 1 5 11 ${FC_dir}/$network/sFC_subj11_post.nii
-dset 1 1 12 ${FC_dir}/$network/sFC_subj12_pre.nii
-dset 1 2 12 ${FC_dir}/$network/sFC_subj12_in1.nii
-dset 1 3 12 ${FC_dir}/$network/sFC_subj12_in2.nii
-dset 1 4 12 ${FC_dir}/$network/sFC_subj12_in3.nii
-dset 1 5 12 ${FC_dir}/$network/sFC_subj12_post.nii
-dset 2 1 1 ${sham_FC_dir}/$network/sham_sFC_subj1_pre.nii
-dset 2 2 1 ${sham_FC_dir}/$network/sham_sFC_subj1_in1.nii
-dset 2 3 1 ${sham_FC_dir}/$network/sham_sFC_subj1_in2.nii
-dset 2 4 1 ${sham_FC_dir}/$network/sham_sFC_subj1_in3.nii
-dset 2 5 1 ${sham_FC_dir}/$network/sham_sFC_subj1_post.nii
-dset 2 1 2 ${sham_FC_dir}/$network/sham_sFC_subj2_pre.nii
-dset 2 2 2 ${sham_FC_dir}/$network/sham_sFC_subj2_in1.nii
-dset 2 3 2 ${sham_FC_dir}/$network/sham_sFC_subj2_in2.nii
-dset 2 4 2 ${sham_FC_dir}/$network/sham_sFC_subj2_in3.nii
-dset 2 5 2 ${sham_FC_dir}/$network/sham_sFC_subj2_post.nii
-dset 2 1 3 ${sham_FC_dir}/$network/sham_sFC_subj3_pre.nii
-dset 2 2 3 ${sham_FC_dir}/$network/sham_sFC_subj3_in1.nii
-dset 2 3 3 ${sham_FC_dir}/$network/sham_sFC_subj3_in2.nii
-dset 2 4 3 ${sham_FC_dir}/$network/sham_sFC_subj3_in3.nii
-dset 2 5 3 ${sham_FC_dir}/$network/sham_sFC_subj3_post.nii
-dset 2 1 4 ${sham_FC_dir}/$network/sham_sFC_subj4_pre.nii
-dset 2 2 4 ${sham_FC_dir}/$network/sham_sFC_subj4_in1.nii
-dset 2 3 4 ${sham_FC_dir}/$network/sham_sFC_subj4_in2.nii
-dset 2 4 4 ${sham_FC_dir}/$network/sham_sFC_subj4_in3.nii
-dset 2 5 4 ${sham_FC_dir}/$network/sham_sFC_subj4_post.nii
-dset 2 1 5 ${sham_FC_dir}/$network/sham_sFC_subj5_pre.nii
-dset 2 2 5 ${sham_FC_dir}/$network/sham_sFC_subj5_in1.nii
-dset 2 3 5 ${sham_FC_dir}/$network/sham_sFC_subj5_in2.nii
-dset 2 4 5 ${sham_FC_dir}/$network/sham_sFC_subj5_in3.nii
-dset 2 5 5 ${sham_FC_dir}/$network/sham_sFC_subj5_post.nii
-dset 2 1 6 ${sham_FC_dir}/$network/sham_sFC_subj6_pre.nii
-dset 2 2 6 ${sham_FC_dir}/$network/sham_sFC_subj6_in1.nii
-dset 2 3 6 ${sham_FC_dir}/$network/sham_sFC_subj6_in2.nii
-dset 2 4 6 ${sham_FC_dir}/$network/sham_sFC_subj6_in3.nii
-dset 2 5 6 ${sham_FC_dir}/$network/sham_sFC_subj6_post.nii
-dset 2 1 7 ${sham_FC_dir}/$network/sham_sFC_subj7_pre.nii
-dset 2 2 7 ${sham_FC_dir}/$network/sham_sFC_subj7_in1.nii
-dset 2 3 7 ${sham_FC_dir}/$network/sham_sFC_subj7_in2.nii
-dset 2 4 7 ${sham_FC_dir}/$network/sham_sFC_subj7_in3.nii
-dset 2 5 7 ${sham_FC_dir}/$network/sham_sFC_subj7_post.nii
-dset 2 1 8 ${sham_FC_dir}/$network/sham_sFC_subj8_pre.nii
-dset 2 2 8 ${sham_FC_dir}/$network/sham_sFC_subj8_in1.nii
-dset 2 3 8 ${sham_FC_dir}/$network/sham_sFC_subj8_in2.nii
-dset 2 4 8 ${sham_FC_dir}/$network/sham_sFC_subj8_in3.nii
-dset 2 5 8 ${sham_FC_dir}/$network/sham_sFC_subj8_post.nii
-dset 2 1 9 ${sham_FC_dir}/$network/sham_sFC_subj9_pre.nii
-dset 2 2 9 ${sham_FC_dir}/$network/sham_sFC_subj9_in1.nii
-dset 2 3 9 ${sham_FC_dir}/$network/sham_sFC_subj9_in2.nii
-dset 2 4 9 ${sham_FC_dir}/$network/sham_sFC_subj9_in3.nii
-dset 2 5 9 ${sham_FC_dir}/$network/sham_sFC_subj9_post.nii
-dset 2 1 10 ${sham_FC_dir}/$network/sham_sFC_subj10_pre.nii
-dset 2 2 10 ${sham_FC_dir}/$network/sham_sFC_subj10_in1.nii
-dset 2 3 10 ${sham_FC_dir}/$network/sham_sFC_subj10_in2.nii
-dset 2 4 10 ${sham_FC_dir}/$network/sham_sFC_subj10_in3.nii
-dset 2 5 10 ${sham_FC_dir}/$network/sham_sFC_subj10_post.nii
-dset 2 1 11 ${sham_FC_dir}/$network/sham_sFC_subj11_pre.nii
-dset 2 2 11 ${sham_FC_dir}/$network/sham_sFC_subj11_in1.nii
-dset 2 3 11 ${sham_FC_dir}/$network/sham_sFC_subj11_in2.nii
-dset 2 4 11 ${sham_FC_dir}/$network/sham_sFC_subj11_in3.nii
-dset 2 5 11 ${sham_FC_dir}/$network/sham_sFC_subj11_post.nii
-dset 2 1 12 ${sham_FC_dir}/$network/sham_sFC_subj12_pre.nii
-dset 2 2 12 ${sham_FC_dir}/$network/sham_sFC_subj12_in1.nii
-dset 2 3 12 ${sham_FC_dir}/$network/sham_sFC_subj12_in2.nii
-dset 2 4 12 ${sham_FC_dir}/$network/sham_sFC_subj12_in3.nii
-dset 2 5 12 ${sham_FC_dir}/$network/sham_sFC_subj12_post.nii
-adiff 1 2 ${out_dir}/${network}/exper_vs_sham.nii
-fa ${out_dir}/${network}/stim_protocol.nii
-fb ${out_dir}/${network}/time.nii
-fab ${out_dir}/${network}/stim_time_interaction.nii
-bucket ${out_dir}/${network}_ANOVA

Thanks in advance!

Tracy

2

Hi Tracy,

It seems likely you are really running out of RAM, and that your other script isn’t using as many datasets or running as many tests or something.

This script will probably use about 1/2 GB RAM.

  • rick
3

Hi Rick,

Thanks for the reply!

I just fixed the problem. It seems not to be related to the RAM.
In my script, for the output part, I have included the path in the output file name. When I removed those path and only included the file name. It worked.
Maybe 3dANOVA3 cannot tolerant path in the output setting?

The change is as follows:
%%%%%
-adiff 1 2 exper_vs_sham
-fa stim_protocol
-fb time
-fab stim_time_interaction
-bucket ANOVA

%%%%%

BTW, I have another question about the results. I’m wondering if the output F-statistics are normalized in the volume? In another way, is it z-transformed?
Or because that the number of voxels are too much, so we don’t need to convert to z scores? Since I need to use another function to do the post analysis and it requires the input to be z-statistics. Sorry that I may be confused about these statistic terms…

Thanks and happy new year!

Tracy

4

Oh, we have noticed that recently. Those older ANOVA programs had heavy restrictions on the lengths of paths. How long was $out_dir?

But I don’t see what a current problem would be (unless out_dir is really long). What does “afni -ver” show?

Thanks,

  • rick
5

Hi Rick,

The total length of the out_dir is 46. And the output of “afni -ver” is “Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 ‘Tiberius’)”

BTW, may I know if the output F-statistics in 3dANOVA3 are normalized in the volume? In another way, is it z-transformed?
Since I need to use another function to do the post analysis and it requires the input to be z-statistics. Can you please suggest about it? Thanks!

Best,
Tracy

6

Okay, this does not seem to be what I thought.

When using a directory for output with -bucket, only that -bucket parameter should have a directory prefix.

At that point, the other entries, such as “-adiff 1 2 exper_vs_sham” are essentially supplying labels. The ‘exper_vs_sham’ text will be the label for related volumes in the bucket dataset.

So when using -bucket, none of the other output options should come with directories. Sorry for the confusion.

  • rick
7

may I know if the output F-statistics in 3dANOVA3 are normalized in the volume?

You can convert an F-statistic sub-brick to Z-statistic with the following steps:

  1. find out the numerator and denominator degrees of freedom for the F-statistic sub-brick

3dAttribute BRICK_STATAUX myFile+tlrc’[##]’

where ## is the F-statistic sub-brick number.

  1. run

3dcalc -a myFile+tlrc’[##]’ -expr ‘fizt_p2t(fift_t2p(a,N1,N2))’ -prefix outputFileName

where ## is the F-statistic sub-brick number, and ‘N1’ and ‘N2’ are the numerator and denominator degrees of freedom from 1) above.

8

Hi Rick,

Thanks for the clarification.

Best,
Tracy

9

Hi Gang,

Many thanks for the reply! It really helps!

I have run 3dAttribute BRICK_STATAUX myFile+tlrc’[##]’ and get the following value:
0 4 2 4 88

After referring to this post (https://afni.nimh.nih.gov/afni/community/board/read.php?1,76015,76017#msg-76017), the numerator and denominator should be 4 and 88 respectively right? The first 4 should be the code for statistics, which is F-stats. But how about 0? What does it mean?

I then run 3dcalc -a myFile+tlrc’[##]’ -expr ‘fizt_p2t(fift_t2p(a,N1,N2))’ -prefix outputFileName as you suggested.
The idea is to first convert f-stats to p value? and then convert p value to z-stats right?

Thanks for your time!

Best,
Tracy

10

After referring to this post (https://afni.nimh.nih.gov/afni/community/board/read.php?1,76015,76017#msg-76017),
the numerator and denominator should be 4 and 88 respectively right?

Yes, that’s correct.

The first 4 should be the code for statistics, which is F-stats. But how about 0? What does it mean?

I’m not sure what the 0 is about, but it’s not important to know in the current context. A couple of more ways to find degrees of freedom:

https://sscc.nimh.nih.gov/sscc/gangc/DF.html

I then run 3dcalc -a myFile+tlrc’[##]’ -expr ‘fizt_p2t(fift_t2p(a,N1,N2))’ -prefix outputFileName as you suggested.
The idea is to first convert f-stats to p value? and then convert p value to z-stats right?

Yes, that’s right.