Hi experts,
I'm trying to denoise my functional multiband data with ICA-AROMA and running into a "buffer overflow" error (see the logfile below). I get all the outputs I'd expect except for the key denoised_func_data.
It seems to be a memory issue, but I'm using a large cluster and even when I send just one run at a time the result is the same. Could it be due to the number of components? There are a lot: in the case below, it found 522 components and classified 384 of them as motion-related. Here are my scanning parameters:
TR = 654 ms
Resolution = 2.5 mm x 2.5 mm x 2.5 mm
54 slices
Multiband acceleration factor = 4
1411 volumes
I've also read that ICA-AROMA can easily get caught up in multiband artefact. Would you recommend running FIX to clean this up before running AROMA? Or any other procedure?
Thank you!
Here's the output I get when trying to run ICA-AROMA:
/home/bgold/.local/lib/python2.7/site-packages/seaborn/categorical.py:462: FutureWarning: remove_na is deprecated and is a private function. Do not use.
box_data = remove_na(group_data)
/home/bgold/.local/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6448: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
warnings.warn("The 'normed' kwarg is deprecated, and has been "
*** buffer overflow detected ***: /usr/share/fsl/5.0/bin/fsl_regfilt terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x145bd58597e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x145bd58fb15c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x145bd58f9160]
/lib/x86_64-linux-gnu/libc.so.6(+0x1164b2)[0x145bd58f84b2]
/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)[0x145bd5802830]
/usr/share/fsl/5.0/bin/fsl_regfilt[0x4081c9]
======= Memory map: ========
00400000-00424000 r-xp 00000000 103:01 17307184 /usr/lib/fsl/5.0/fsl_regfilt
00623000-00624000 r--p 00023000 103:01 17307184 /usr/lib/fsl/5.0/fsl_regfilt
00624000-00625000 rw-p 00024000 103:01 17307184 /usr/lib/fsl/5.0/fsl_regfilt
00625000-00626000 rw-p 00000000 00:00 0
00917000-135a6000 rw-p 00000000 00:00 0 [heap]
1459d4236000-145ad47f2000 rw-p 00000000 00:00 0
145bd4f93000-145bd4fae000 r-xp 00000000 103:01 8395294 /opt/minc_20180813/1.9.16/lib/libz.so.1.2.11
145bd4fae000-145bd51ad000 ---p 0001b000 103:01 8395294 /opt/minc_20180813/1.9.16/lib/libz.so.1.2.11
145bd51ad000-145bd51ae000 r--p 0001a000 103:01 8395294 /opt/minc_20180813/1.9.16/lib/libz.so.1.2.11
145bd51ae000-145bd51af000 rw-p 0001b000 103:01 8395294 /opt/minc_20180813/1.9.16/lib/libz.so.1.2.11
145bd51af000-145bd51b2000 r-xp 00000000 103:01 16919398 /usr/lib/libznz.so.2.0.0
145bd51b2000-145bd53b1000 ---p 00003000 103:01 16919398 /usr/lib/libznz.so.2.0.0
145bd53b1000-145bd53b2000 r--p 00002000 103:01 16919398 /usr/lib/libznz.so.2.0.0
145bd53b2000-145bd53b3000 rw-p 00003000 103:01 16919398 /usr/lib/libznz.so.2.0.0
145bd53b3000-145bd53d3000 r-xp 00000000 103:01 16919396 /usr/lib/libniftiio.so.2.0.0
145bd53d3000-145bd55d3000 ---p 00020000 103:01 16919396 /usr/lib/libniftiio.so.2.0.0
145bd55d3000-145bd55d4000 r--p 00020000 103:01 16919396 /usr/lib/libniftiio.so.2.0.0
145bd55d4000-145bd55d5000 rw-p 00021000 103:01 16919396 /usr/lib/libniftiio.so.2.0.0
145bd55d5000-145bd55e1000 r-xp 00000000 103:01 17307397 /usr/lib/fsl/5.0/libfslio.so
145bd55e1000-145bd57e0000 ---p 0000c000 103:01 17307397 /usr/lib/fsl/5.0/libfslio.so
145bd57e0000-145bd57e1000 r--p 0000b000 103:01 17307397 /usr/lib/fsl/5.0/libfslio.so
145bd57e1000-145bd57e2000 rw-p 0000c000 103:01 17307397 /usr/lib/fsl/5.0/libfslio.so
145bd57e2000-145bd59a2000 r-xp 00000000 103:01 17432660 /lib/x86_64-linux-gnu/libc-2.23.so
145bd59a2000-145bd5ba2000 ---p 001c0000 103:01 17432660 /lib/x86_64-linux-gnu/libc-2.23.so
145bd5ba2000-145bd5ba6000 r--p 001c0000 103:01 17432660 /lib/x86_64-linux-gnu/libc-2.23.so
145bd5ba6000-145bd5ba8000 rw-p 001c4000 103:01 17432660 /lib/x86_64-linux-gnu/libc-2.23.so
145bd5ba8000-145bd5bac000 rw-p 00000000 00:00 0
145bd5bac000-145bd5bc2000 r-xp 00000000 103:01 17437149 /lib/x86_64-linux-gnu/libgcc_s.so.1
145bd5bc2000-145bd5dc1000 ---p 00016000 103:01 17437149 /lib/x86_64-linux-gnu/libgcc_s.so.1
145bd5dc1000-145bd5dc2000 rw-p 00015000 103:01 17437149 /lib/x86_64-linux-gnu/libgcc_s.so.1
145bd5dc2000-145bd5eca000 r-xp 00000000 103:01 17432590 /lib/x86_64-linux-gnu/libm-2.23.so
145bd5eca000-145bd60c9000 ---p 00108000 103:01 17432590 /lib/x86_64-linux-gnu/libm-2.23.so
145bd60c9000-145bd60ca000 r--p 00107000 103:01 17432590 /lib/x86_64-linux-gnu/libm-2.23.so
145bd60ca000-145bd60cb000 rw-p 00108000 103:01 17432590 /lib/x86_64-linux-gnu/libm-2.23.so
145bd60cb000-145bd623d000 r-xp 00000000 103:01 16910469 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
145bd623d000-145bd643d000 ---p 00172000 103:01 16910469 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
145bd643d000-145bd6447000 r--p 00172000 103:01 16910469 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
145bd6447000-145bd6449000 rw-p 0017c000 103:01 16910469 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
145bd6449000-145bd644d000 rw-p 00000000 00:00 0
145bd644d000-145bd6454000 r-xp 00000000 103:01 17307337 /usr/lib/fsl/5.0/libprob.so
145bd6454000-145bd6653000 ---p 00007000 103:01 17307337 /usr/lib/fsl/5.0/libprob.so
145bd6653000-145bd6654000 r--p 00006000 103:01 17307337 /usr/lib/fsl/5.0/libprob.so
145bd6654000-145bd6655000 rw-p 00007000 103:01 17307337 /usr/lib/fsl/5.0/libprob.so
145bd6655000-145bd66a7000 r-xp 00000000 103:01 16919404 /usr/lib/libnewmat.so.10.0.0
145bd66a7000-145bd68a7000 ---p 00052000 103:01 16919404 /usr/lib/libnewmat.so.10.0.0
145bd68a7000-145bd68ab000 r--p 00052000 103:01 16919404 /usr/lib/libnewmat.so.10.0.0
145bd68ab000-145bd68ac000 rw-p 00056000 103:01 16919404 /usr/lib/libnewmat.so.10.0.0
145bd68ac000-145bd6939000 r-xp 00000000 103:01 17307205 /usr/lib/fsl/5.0/libmiscmaths.so
145bd6939000-145bd6b39000 ---p 0008d000 103:01 17307205 /usr/lib/fsl/5.0/libmiscmaths.so
145bd6b39000-145bd6b3a000 r--p 0008d000 103:01 17307205 /usr/lib/fsl/5.0/libmiscmaths.so
145bd6b3a000-145bd6b3b000 rw-p 0008e000 103:01 17307205 /usr/lib/fsl/5.0/libmiscmaths.so
145bd6b3b000-145bd6cb0000 r-xp 00000000 103:01 17307142 /usr/lib/fsl/5.0/libnewimage.so
145bd6cb0000-145bd6eb0000 ---p 00175000 103:01 17307142 /usr/lib/fsl/5.0/libnewimage.so
145bd6eb0000-145bd6eb1000 r--p 00175000 103:01 17307142 /usr/lib/fsl/5.0/libnewimage.so
145bd6eb1000-145bd6eb2000 rw-p 00176000 103:01 17307142 /usr/lib/fsl/5.0/libnewimage.so
145bd6eb2000-145bd6eb3000 rw-p 00000000 00:00 0
145bd6eb3000-145bd6ebf000 r-xp 00000000 103:01 17307164 /usr/lib/fsl/5.0/libutils.so
145bd6ebf000-145bd70be000 ---p 0000c000 103:01 17307164 /usr/lib/fsl/5.0/libutils.so
145bd70be000-145bd70bf000 r--p 0000b000 103:01 17307164 /usr/lib/fsl/5.0/libutils.so
145bd70bf000-145bd70c0000 rw-p 0000c000 103:01 17307164 /usr/lib/fsl/5.0/libutils.so
145bd70c0000-145bd70e6000 r-xp 00000000 103:01 17432601 /lib/x86_64-linux-gnu/ld-2.23.so
145bd72be000-145bd72c7000 rw-p 00000000 00:00 0
145bd72e3000-145bd72e5000 rw-p 00000000 00:00 0
145bd72e5000-145bd72e6000 r--p 00025000 103:01 17432601 /lib/x86_64-linux-gnu/ld-2.23.so
145bd72e6000-145bd72e7000 rw-p 00026000 103:01 17432601 /lib/x86_64-linux-gnu/ld-2.23.so
145bd72e7000-145bd72e8000 rw-p 00000000 00:00 0
7ffd63a12000-7ffd63a34000 rw-p 00000000 00:00 0 [stack]
7ffd63be2000-7ffd63be5000 r--p 00000000 00:00 0 [vvar]
7ffd63be5000-7ffd63be7000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
------------------------------- RUNNING ICA-AROMA -------------------------------
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------
Step 1) MELODIC
Step 2) Automatic classification of the components
- registering the spatial maps to MNI
- extracting the CSF & Edge fraction features
- extracting the Maximum RP correlation feature
- extracting the High-frequency content feature
- classification
Found 1 file(s)
Found 384 head motion-related components in a total of 522 components.
Step 3) Data denoising
----------------------------------- Finished -----------------------------------
########################################################################
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