Buffer overflow during fmriprep 1.0.0-rc2

,
1

Hi all,
I conducted the preprocessing of my fMRI data using fmriprep 1.0.0-rc2 (on Ubuntu 14.04 (128GB RAM, 22C/44T CPU)).
In the steps of ICA-AROMA, only a part of subjects showed following error related with the buffer overflow.
I have tried several options (–nthreads or --omp-nthreads), but cannot pass this error.
Any suggestions would be highly appreciated.

Sincerely,
Yuki

*** buffer overflow detected ***: /usr/share/fsl/5.0/bin/fsl_regfilt terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f0ea667c7e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f0ea671d56c]
/lib/x86_64-linux-gnu/libc.so.6(+0x116570)[0x7f0ea671b570]
/lib/x86_64-linux-gnu/libc.so.6(+0x1158c2)[0x7f0ea671a8c2]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x413d5f]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x416d35]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x416f12]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x408061]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f0ea6625830]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x4081c9]
======= Memory map: ========
00400000-00424000 r-xp 00000000 00:23 5710 /usr/lib/fsl/5.0/fsl_regfilt
00623000-00624000 r–p 00023000 00:23 5710 /usr/lib/fsl/5.0/fsl_regfilt
00624000-00625000 rw-p 00024000 00:23 5710 /usr/lib/fsl/5.0/fsl_regfilt
00625000-00626000 rw-p 00000000 00:00 0
011b1000-373d6000 rw-p 00000000 00:00 0 [heap]
7f0e3f3ca000-7f0e728c1000 rw-p 00000000 00:00 0
7f0ea5db8000-7f0ea5dd1000 r-xp 00000000 00:23 5214 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f0ea5dd1000-7f0ea5fd0000 —p 00019000 00:23 5214 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f0ea5fd0000-7f0ea5fd1000 r–p 00018000 00:23 5214 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f0ea5fd1000-7f0ea5fd2000 rw-p 00019000 00:23 5214 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f0ea5fd2000-7f0ea5fd5000 r-xp 00000000 00:23 5224 /usr/lib/libznz.so.2.0.0
7f0ea5fd5000-7f0ea61d4000 —p 00003000 00:23 5224 /usr/lib/libznz.so.2.0.0
7f0ea61d4000-7f0ea61d5000 r–p 00002000 00:23 5224 /usr/lib/libznz.so.2.0.0
7f0ea61d5000-7f0ea61d6000 rw-p 00003000 00:23 5224 /usr/lib/libznz.so.2.0.0
7f0ea61d6000-7f0ea61f6000 r-xp 00000000 00:23 5212 /usr/lib/libniftiio.so.2.0.0
7f0ea61f6000-7f0ea63f6000 —p 00020000 00:23 5212 /usr/lib/libniftiio.so.2.0.0
7f0ea63f6000-7f0ea63f7000 r–p 00020000 00:23 5212 /usr/lib/libniftiio.so.2.0.0
7f0ea63f7000-7f0ea63f8000 rw-p 00021000 00:23 5212 /usr/lib/libniftiio.so.2.0.0
7f0ea63f8000-7f0ea6404000 r-xp 00000000 00:23 5584 /usr/lib/fsl/5.0/libfslio.so
7f0ea6404000-7f0ea6603000 —p 0000c000 00:23 5584 /usr/lib/fsl/5.0/libfslio.so
7f0ea6603000-7f0ea6604000 r–p 0000b000 00:23 5584 /usr/lib/fsl/5.0/libfslio.so
7f0ea6604000-7f0ea6605000 rw-p 0000c000 00:23 5584 /usr/lib/fsl/5.0/libfslio.so
7f0ea6605000-7f0ea67c4000 r-xp 00000000 00:23 55 /lib/x86_64-linux-gnu/libc-2.23.so
7f0ea67c4000-7f0ea69c4000 —p 001bf000 00:23 55 /lib/x86_64-linux-gnu/libc-2.23.so
7f0ea69c4000-7f0ea69c8000 r–p 001bf000 00:23 55 /lib/x86_64-linux-gnu/libc-2.23.so
7f0ea69c8000-7f0ea69ca000 rw-p 001c3000 00:23 55 /lib/x86_64-linux-gnu/libc-2.23.so
7f0ea69ca000-7f0ea69ce000 rw-p 00000000 00:00 0
7f0ea69ce000-7f0ea69e4000 r-xp 00000000 00:23 9628 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f0ea69e4000-7f0ea6be3000 —p 00016000 00:23 9628 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f0ea6be3000-7f0ea6be4000 rw-p 00015000 00:23 9628 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f0ea6be4000-7f0ea6cec000 r-xp 00000000 00:23 53 /lib/x86_64-linux-gnu/libm-2.23.so
7f0ea6cec000-7f0ea6eeb000 —p 00108000 00:23 53 /lib/x86_64-linux-gnu/libm-2.23.so
7f0ea6eeb000-7f0ea6eec000 r–p 00107000 00:23 53 /lib/x86_64-linux-gnu/libm-2.23.so
7f0ea6eec000-7f0ea6eed000 rw-p 00108000 00:23 53 /lib/x86_64-linux-gnu/libm-2.23.so
7f0ea6eed000-7f0ea705f000 r-xp 00000000 00:23 9627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f0ea705f000-7f0ea725f000 —p 00172000 00:23 9627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f0ea725f000-7f0ea7269000 r–p 00172000 00:23 9627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f0ea7269000-7f0ea726b000 rw-p 0017c000 00:23 9627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f0ea726b000-7f0ea726f000 rw-p 00000000 00:00 0
7f0ea726f000-7f0ea7276000 r-xp 00000000 00:23 5781 /usr/lib/fsl/5.0/libprob.so
7f0ea7276000-7f0ea7475000 —p 00007000 00:23 5781 /usr/lib/fsl/5.0/libprob.so
7f0ea7475000-7f0ea7476000 r–p 00006000 00:23 5781 /usr/lib/fsl/5.0/libprob.so
7f0ea7476000-7f0ea7477000 rw-p 00007000 00:23 5781 /usr/lib/fsl/5.0/libprob.so
7f0ea7477000-7f0ea74c9000 r-xp 00000000 00:23 19333 /usr/lib/libnewmat.so.10.0.0
7f0ea74c9000-7f0ea76c9000 —p 00052000 00:23 19333 /usr/lib/libnewmat.so.10.0.0
7f0ea76c9000-7f0ea76cd000 r–p 00052000 00:23 19333 /usr/lib/libnewmat.so.10.0.0
7f0ea76cd000-7f0ea76ce000 rw-p 00056000 00:23 19333 /usr/lib/libnewmat.so.10.0.0
7f0ea76ce000-7f0ea775b000 r-xp 00000000 00:23 5527 /usr/lib/fsl/5.0/libmiscmaths.so
7f0ea775b000-7f0ea795b000 —p 0008d000 00:23 5527 /usr/lib/fsl/5.0/libmiscmaths.so
7f0ea795b000-7f0ea795c000 r–p 0008d000 00:23 5527 /usr/lib/fsl/5.0/libmiscmaths.so
7f0ea795c000-7f0ea795d000 rw-p 0008e000 00:23 5527 /usr/lib/fsl/5.0/libmiscmaths.so
7f0ea795d000-7f0ea7ad2000 r-xp 00000000 00:23 5559 /usr/lib/fsl/5.0/libnewimage.so
7f0ea7ad2000-7f0ea7cd2000 —p 00175000 00:23 5559 /usr/lib/fsl/5.0/libnewimage.so
7f0ea7cd2000-7f0ea7cd3000 r–p 00175000 00:23 5559 /usr/lib/fsl/5.0/libnewimage.so
7f0ea7cd3000-7f0ea7cd4000 rw-p 00176000 00:23 5559 /usr/lib/fsl/5.0/libnewimage.so
7f0ea7cd4000-7f0ea7cd5000 rw-p 00000000 00:00 0
7f0ea7cd5000-7f0ea7ce1000 r-xp 00000000 00:23 5536 /usr/lib/fsl/5.0/libutils.so
7f0ea7ce1000-7f0ea7ee0000 —p 0000c000 00:23 5536 /usr/lib/fsl/5.0/libutils.so
7f0ea7ee0000-7f0ea7ee1000 r–p 0000b000 00:23 5536 /usr/lib/fsl/5.0/libutils.so
7f0ea7ee1000-7f0ea7ee2000 rw-p 0000c000 00:23 5536 /usr/lib/fsl/5.0/libutils.so
7f0ea7ee2000-7f0ea7f08000 r-xp 00000000 00:23 37 /lib/x86_64-linux-gnu/ld-2.23.so
7f0ea80f4000-7f0ea80fc000 rw-p 00000000 00:00 0
7f0ea8103000-7f0ea8107000 rw-p 00000000 00:00 0
7f0ea8107000-7f0ea8108000 r–p 00025000 00:23 37 /lib/x86_64-linux-gnu/ld-2.23.so
7f0ea8108000-7f0ea8109000 rw-p 00026000 00:23 37 /lib/x86_64-linux-gnu/ld-2.23.so
7f0ea8109000-7f0ea810a000 rw-p 00000000 00:00 0
7ffe990d5000-7ffe990f6000 rw-p 00000000 00:00 0 [stack]
7ffe991bc000-7ffe991be000 r–p 00000000 00:00 0 [vvar]
7ffe991be000-7ffe991c0000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

2

This seems relevant: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&P=R83070&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4

Especially the reply:

It does complete now - the dataset I was testing this on had 299 components to filter (its a multiband BOLD data set with ~1500 volumes so melodic finds >600 components in the data). I’ve narrowed it down and fsl_regfilt can run a maximum of 270 components (with this subject data at least).

Is it valid therefore to run this command on all my other subjects data, reducing the filtered components to 270 (not including the smallest ones, i.e. those which explain the smallest amount of variance)?

How many TRs does your input data have?

One solution would be reimplementing fsl_regfilt in pure python to support such big data.

3

Thank you very much. The error you suggested is completely same as my case.
My data is about 900 volumes and too much components must be the problem.
So, fmriprep 1.0.0-rc2 cannot deal with this kinds of big data when we want to use ICA-AROMA due to the external function fsl_regfilt. Is my understanding correct?

4

I’m afraid so. This will be the case until fsl_regfilt will be fixed or replaced.

5

Thank you very much! I understand.