I don't think our sever is running out of memory.
It is related to applyxfm; I got the same error message when I just run applyxfm with the same BPmap (the input image).
Do you think a specific image can cause this error?
I ran the same procedure with additional 51 images (BPmaps) without error.
Thank you,
Buyean
/usr/local/fsl/bin/flirt -in /data/pet/Fallypride/BPmap/FSL_normalization/rsl_images_SPM_coreg/8201_scan1_Logan_a1_BPnd.nii -applyxfm -init /data/pet/Fallypride/BPmap/FSL_normalization/rsl_images_SPM_coreg/r8201_AX_CROP_AC_to_std_sub.mat -out /data/pet/Fallypride/BPmap/FSL_normalization/rsl_images_SPM_coreg/rFSL_8201_scan1_Logan_a1_BPnd.nii -paddingsize 0.0 -interp trilinear -ref /data/pet/Fallypride/BPmap/SPM_normalization/FSLtemp_1mm_MNI_normalzation/MNI152_T1_1mm.nii
*** glibc detected *** /usr/local/fsl/bin/flirt: double free or corruption (out): 0x00000000059b0020 ***
======= Backtrace: =========
/lib64/libc.so.6[0x354e471ce2]
/lib64/libc.so.6(cfree+0x8c)[0x354e47590c]
/usr/local/fsl/bin/flirt[0x481f5b]
/usr/local/fsl/bin/flirt[0x4226fe]
/usr/local/fsl/bin/flirt[0x40b852]
/usr/local/fsl/bin/flirt[0x41b157]
/usr/local/fsl/bin/flirt[0x41f1a5]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x354e41d974]
/usr/local/fsl/bin/flirt(__gxx_personality_v0+0x139)[0x403ae9]
======= Memory map: ========
00400000-005df000 r-xp 00000000 09:00 255312310 /usr/local/fsl/bin/flirt
007df000-007e0000 rw-p 001df000 09:00 255312310 /usr/local/fsl/bin/flirt
007e0000-007e2000 rw-p 007e0000 00:00 0
05393000-06c14000 rw-p 05393000 00:00 0 [heap]
354e000000-354e01c000 r-xp 00000000 03:01 641290 /lib64/ld-2.5.so
354e21b000-354e21c000 r--p 0001b000 03:01 641290 /lib64/ld-2.5.so
354e21c000-354e21d000 rw-p 0001c000 03:01 641290 /lib64/ld-2.5.so
354e400000-354e54c000 r-xp 00000000 03:01 641300 /lib64/libc-2.5.so
354e54c000-354e74c000 ---p 0014c000 03:01 641300 /lib64/libc-2.5.so
354e74c000-354e750000 r--p 0014c000 03:01 641300 /lib64/libc-2.5.so
354e750000-354e751000 rw-p 00150000 03:01 641300 /lib64/libc-2.5.so
354e751000-354e756000 rw-p 354e751000 00:00 0
354ec00000-354ec82000 r-xp 00000000 03:01 641439 /lib64/libm-2.5.so
354ec82000-354ee81000 ---p 00082000 03:01 641439 /lib64/libm-2.5.so
354ee81000-354ee82000 r--p 00081000 03:01 641439 /lib64/libm-2.5.so
354ee82000-354ee83000 rw-p 00082000 03:01 641439 /lib64/libm-2.5.so
3557000000-355700d000 r-xp 00000000 03:01 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
355700d000-355720d000 ---p 0000d000 03:01 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
355720d000-355720e000 rw-p 0000d000 03:01 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
355be00000-355bee6000 r-xp 00000000 03:01 135033 /usr/lib64/libstdc++.so.6.0.8
355bee6000-355c0e5000 ---p 000e6000 03:01 135033 /usr/lib64/libstdc++.so.6.0.8
355c0e5000-355c0eb000 r--p 000e5000 03:01 135033 /usr/lib64/libstdc++.so.6.0.8
355c0eb000-355c0ee000 rw-p 000eb000 03:01 135033 /usr/lib64/libstdc++.so.6.0.8
355c0ee000-355c100000 rw-p 355c0ee000 00:00 0
2acef0f62000-2acef0f63000 rw-p 2acef0f62000 00:00 0
2acef0f70000-2acef468b000 rw-p 2acef0f70000 00:00 0
2acef8000000-2acef8021000 rw-p 2acef8000000 00:00 0
2acef8021000-2acefc000000 ---p 2acef8021000 00:00 0
7fffb9b33000-7fffb9b48000 rw-p 7ffffffea000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
child killed: SIGABRT
No output saved!
Done
-----Original Message-----
From: Mark Jenkinson <[log in to unmask]>
To: [log in to unmask]
Sent: Mon, 2 Mar 2009 12:11 am
Subject: Re: [FSL] first_flirt error
Hi,
This looks really unusual - I've never seen it before.
It looks like you have a problem with memory. Either it is
running out or there is a fault in your memory. We once
saw something similar with a machine that had defective
memory. Just try this again and see if it works or not.
All the best,
Mark
On 2 Mar 2009, at 06:08, Buyean Lee wrote:
> Dear FSL users,
>
> I am evaluating if 'first_flirt' can better spatially normalize the > subcortical structures than regular normalization.
> I am interested in this because the PET images that I use have main > activities in the subcortical areas.
>
> Briefly, the PET images are spatially normalized with the > transformation matrix that I can get by running 'first_flirt' with > the T1 MRI (coregistered (and resliced) to a PET image).
> It worked in most scans, but in one scan I met the following error > messages.
> I will appreciate suggestion to resolve this problem.
>
> Thank you,
>
> Buyean
>
> initial registration 0
> Stage 2: use subcortical mask
> The output image will use the sform from the reference image
> Init Matrix =
> 1.063290 0.007515 0.034482 -43.099900
> 0.006513 1.099080 0.184719 -58.276500
> -0.044797 -0.205962 1.193220 -15.086300
> 0.000000 0.000000 0.000000 1.000000
>
> *** glibc detected *** flirt: munmap_chunk(): invalid pointer: > 0x0000000003a67ad0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6(cfree+0x1b6)[0x354e475a36]
> flirt[0x481f5b]
> flirt[0x4226fe]
> flirt[0x40b852]
> flirt[0x41b157]
> flirt[0x41f1a5]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x354e41d974]
> flirt(__gxx_personality_v0+0x139)[0x403ae9]
> ======= Memory map: ========
> 00400000-005df000 r-xp 00000000 09:00 > 255312310 /usr/local/fsl/bin/flirt
> 007df000-007e0000 rw-p 001df000 09:00 > 255312310 /usr/local/fsl/bin/flirt
> 007e0000-007e2000 rw-p 007e0000 00:00 0
> 0343d000-04cbe000 rw-p 0343d000 00:00 > 0 [heap]
> 354e000000-354e01c000 r-xp 00000000 03:01 > 641290 /lib64/ld-2.5.so
> 354e21b000-354e21c000 r--p 0001b000 03:01 > 641290 /lib64/ld-2.5.so
> 354e21c000-354e21d000 rw-p 0001c000 03:01 > 641290 /lib64/ld-2.5.so
> 354e400000-354e54c000 r-xp 00000000 03:01 > 641300 /lib64/libc-2.5.so
> 354e54c000-354e74c000 ---p 0014c000 03:01 > 641300 /lib64/libc-2.5.so
> 354e74c000-354e750000 r--p 0014c000 03:01 > 641300 /lib64/libc-2.5.so
> 354e750000-354e751000 rw-p 00150000 03:01 > 641300 /lib64/libc-2.5.so
> 354e751000-354e756000 rw-p 354e751000 00:00 0
> 354ec00000-354ec82000 r-xp 00000000 03:01 > 641439 /lib64/libm-2.5.so
> 354ec82000-354ee81000 ---p 00082000 03:01 > 641439 /lib64/libm-2.5.so
> 354ee81000-354ee82000 r--p 00081000 03:01 > 641439 /lib64/libm-2.5.so
> 354ee82000-354ee83000 rw-p 00082000 03:01 > 641439 /lib64/libm-2.5.so
> 3557000000-355700d000 r-xp 00000000 03:01 > 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
> 355700d000-355720d000 ---p 0000d000 03:01 > 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
> 355720d000-355720e000 rw-p 0000d000 03:01 > 641469 /lib64/libgcc_s-4.1.2-20080825.so.1
> 355be00000-355bee6000 r-xp 00000000 03:01 > 135033 /usr/lib64/libstdc++.so.6.0.8
> 355bee6000-355c0e5000 ---p 000e6000 03:01 > 135033 /usr/lib64/libstdc++.so.6.0.8
> 355c0e5000-355c0eb000 r--p 000e5000 03:01 > 135033 /usr/lib64/libstdc++.so.6.0.8
> 355c0eb000-355c0ee000 rw-p 000eb000 03:01 > 135033 /usr/lib64/libstdc++.so.6.0.8
> 355c0ee000-355c100000 rw-p 355c0ee000 00:00 0
> 2b9fd76f0000-2b9fd76f2000 rw-p 2b9fd76f0000 00:00 0
> 2b9fd76fe000-2b9fdae19000 rw-p 2b9fd76fe000 00:00 0
> 7fffd33a5000-7fffd33ba000 rw-p 7ffffffea000 00:00 > 0 [stack]
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 > 0 [vdso]
> ../applyxfm_1stflirt: line 18: 22959 Aborted flirt -> in $applyxfm_input -applyxfm -init $f4.mat -out rFSL_$> {applyxfm_input} -paddingsize 0.0 -interp sinc -sincwidth 7 -> sincwindow hanning -ref $f4.nii -v
>
>
>
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