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  

|
January 09, 2018 04:22PM
Thanks for your feedback. I tried running 3dNetCorr with these parameters :

3dNetCorr \
-inset pc09.p64_rest_run1_MEICA.spc.nii.gz \
-in_rois test_resamp_addtROI_2func+tlrc. test_resamp_audcatROI_2func+tlrc. \
-fish_z -ts_wb_corr -mask p64_rest_run1.REF.mask.FBrain.MNI.nii.gz \
-prefix test_p64_netcorr

and I got this error:
++ Reading in.
++ Allocating...
++ User didn't enter mask: will make my own, based on where I find nonzero time series.
++ Applying mask to ROIs.
++ Labelling regions internally.
++ No refset labeltable for naming things.
++ Getting volumes.
++ Calculating average time series.
++ Calculating correlation matrix.
++ Writing output: NETCORR ...
*** glibc detected *** 3dNetCorr: munmap_chunk(): invalid pointer: 0x00000000008a4eb7 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3770675dee]
3dNetCorr[0x477066]
3dNetCorr[0x40b79f]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x377061ed1d]
3dNetCorr[0x408459]
======= Memory map: ========
00400000-0092c000 r-xp 00000000 00:18 194457613 /usr/local/apps/afni/current/linux_openmp_64/3dNetCorr
00b2c000-00b76000 rw-p 0052c000 00:18 194457613 /usr/local/apps/afni/current/linux_openmp_64/3dNetCorr
00b76000-00bcf000 rw-p 00000000 00:00 0
01fe4000-27489000 rw-p 00000000 00:00 0 [heap]
3770200000-3770220000 r-xp 00000000 fd:01 393407 /lib64/ld-2.12.so
3770420000-3770421000 r--p 00020000 fd:01 393407 /lib64/ld-2.12.so
3770421000-3770422000 rw-p 00021000 fd:01 393407 /lib64/ld-2.12.so
3770422000-3770423000 rw-p 00000000 00:00 0
3770600000-377078a000 r-xp 00000000 fd:01 400596 /lib64/libc-2.12.so
377078a000-377098a000 ---p 0018a000 fd:01 400596 /lib64/libc-2.12.so
377098a000-377098e000 r--p 0018a000 fd:01 400596 /lib64/libc-2.12.so
377098e000-3770990000 rw-p 0018e000 fd:01 400596 /lib64/libc-2.12.so
3770990000-3770994000 rw-p 00000000 00:00 0
3770a00000-3770a83000 r-xp 00000000 fd:01 410346 /lib64/libm-2.12.so
3770a83000-3770c82000 ---p 00083000 fd:01 410346 /lib64/libm-2.12.so
3770c82000-3770c83000 r--p 00082000 fd:01 410346 /lib64/libm-2.12.so
3770c83000-3770c84000 rw-p 00083000 fd:01 410346 /lib64/libm-2.12.so
3770e00000-3770e02000 r-xp 00000000 fd:01 410258 /lib64/libdl-2.12.so
3770e02000-3771002000 ---p 00002000 fd:01 410258 /lib64/libdl-2.12.so
3771002000-3771003000 r--p 00002000 fd:01 410258 /lib64/libdl-2.12.so
3771003000-3771004000 rw-p 00003000 fd:01 410258 /lib64/libdl-2.12.so
3771200000-3771208000 r-xp 00000000 fd:01 1360346 /usr/lib64/libXp.so.6.2.0
3771208000-3771407000 ---p 00008000 fd:01 1360346 /usr/lib64/libXp.so.6.2.0
3771407000-3771408000 rw-p 00007000 fd:01 1360346 /usr/lib64/libXp.so.6.2.0
3771600000-3771615000 r-xp 00000000 fd:01 410327 /lib64/libz.so.1.2.3
3771615000-3771814000 ---p 00015000 fd:01 410327 /lib64/libz.so.1.2.3
3771814000-3771815000 r--p 00014000 fd:01 410327 /lib64/libz.so.1.2.3
3771815000-3771816000 rw-p 00015000 fd:01 410327 /lib64/libz.so.1.2.3
3773200000-3773224000 r-xp 00000000 fd:01 1352579 /usr/lib64/libxcb.so.1.1.0
3773224000-3773424000 ---p 00024000 fd:01 1352579 /usr/lib64/libxcb.so.1.1.0
3773424000-3773425000 rw-p 00024000 fd:01 1352579 /usr/lib64/libxcb.so.1.1.0
3773600000-3773737000 r-xp 00000000 fd:01 1323296 /usr/lib64/libX11.so.6.3.0
3773737000-3773937000 ---p 00137000 fd:01 1323296 /usr/lib64/libX11.so.6.3.0
3773937000-377393d000 rw-p 00137000 fd:01 1323296 /usr/lib64/libX11.so.6.3.0
3773a00000-3773a02000 r-xp 00000000 fd:01 1313334 /usr/lib64/libXau.so.6.0.0
3773a02000-3773c02000 ---p 00002000 fd:01 1313334 /usr/lib64/libXau.so.6.0.0
3773c02000-3773c03000 rw-p 00002000 fd:01 1313334 /usr/lib64/libXau.so.6.0.0
3774200000-3774298000 r-xp 00000000 fd:01 1360315 /usr/lib64/libfreetype.so.6.3.22
3774298000-3774497000 ---p 00098000 fd:01 1360315 /usr/lib64/libfreetype.so.6.3.22
3774497000-377449d000 rw-p 00097000 fd:01 1360315 /usr/lib64/libfreetype.so.6.3.22
3774600000-3774626000 r-xp 00000000 fd:01 410416 /lib64/libexpat.so.1.5.2
3774626000-3774825000 ---p 00026000 fd:01 410416 /lib64/libexpat.so.1.5.2
3774825000-3774828000 rw-p 00025000 fd:01 410416 /lib64/libexpat.so.1.5.2
3774a00000-3774a11000 r-xp 00000000 fd:01 1360289 /usr/lib64/libXext.so.6.4.0
3774a11000-3774c11000 ---p 00011000 fd:01 1360289 /usr/lib64/libXext.so.6.4.0
3774c11000-3774c12000 rw-p 00011000 fd:01 1360289 /usr/lib64/libXext.so.6.4.0
3774e00000-3774e34000 r-xp 00000000 fd:01 1360316 /usr/lib64/libfontconfig.so.1.4.4
3774e34000-3775034000 ---p 00034000 fd:01 1360316 /usr/lib64/libfontconfig.so.1.4.4
3775034000-3775036000 rw-p 00034000 fd:01 1360316 /usr/lib64/libfontconfig.so.1.4.4
3775200000-3775225000 r-xp 00000000 fd:01 1360317 /usr/lib64/libpng12.so.0.49.0
3775225000-3775425000 ---p 00025000 fd:01 1360317 /usr/lib64/libpng12.so.0.49.0
3775425000-3775426000 rw-p 00025000 fd:01 1360317 /usr/lib64/libpng12.so.0.49.0
3775600000-3775609000 r-xp 00000000 fd:01 1360303 /usr/lib64/libXrender.so.1.3.0
3775609000-3775808000 ---p 00009000 fd:01 1360303 /usr/lib64/libXrender.so.1.3.0
3775808000-3775809000 rw-p 00008000 fd:01 1360303 /usr/lib64/libXrender.so.1.3.0
3776200000-3776216000 r-xp 00000000 fd:01 410365 /lib64/libgcc_s-4.4.7-20120601.so.1
3776216000-3776415000 ---p 00016000 fd:01 410365 /lib64/libgcc_s-4.4.7-20120601.so.1
3776415000-3776416000 rw-p 00015000 fd:01 410365 /lib64/libgcc_s-4.4.7-20120601.so.1
377d200000-377d211000 r-xp 00000000 fd:01 1347097 /usr/lib64/libXpm.so.4.11.0
377d211000-377d410000 ---p 00011000 fd:01 1347097 /usr/lib64/libXpm.so.4.11.0
377d410000-377d411000 rw-p 00010000 fd:01 1347097 /usr/lib64/libXpm.so.4.11.0
377e200000-377e214000 r-xp 00000000 fd:01 1360347 /usr/lib64/libXft.so.2.3.2
377e214000-377e414000 ---p 00014000 fd:01 1360347 /usr/lib64/libXft.so.2.3.2
Fatal Signal 6 (SIGABRT) received
Bottom of Debug Stack
** AFNI version = AFNI_18.0.00 Compile date = Jan 4 2018
** [[Precompiled binary linux_openmp_64: Jan 4 2018]]
** Program Death **


I have no clue what to make of this, help would be much appreciated :)
Subject Author Posted

ROI file format in 3dTcorr1D and 3dNetCorr

rolinskira January 08, 2018 04:04PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

ptaylor January 08, 2018 04:52PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

rolinskira January 09, 2018 04:22PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

ptaylor January 09, 2018 04:26PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

rolinskira January 09, 2018 05:39PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

ptaylor January 09, 2018 06:02PM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

ptaylor January 10, 2018 11:10AM

Re: ROI file format in 3dTcorr1D and 3dNetCorr

rolinskira January 10, 2018 05:22PM