Hi,
It is possible that if the images contain non-numbers (e.g. NaN) then
this might cause some problems. I believe that SPM uses these codes
for implicit masking, and as I see SPM in your filenames, I guess that
might be the cause. To remove these run:
fslmaths inputimage -nan outputimage
If you try the command again (using the newly formed image from
the above fslmaths call) then hopefully it will work. If not, please
upload the images to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
All the best,
Mark
On 3 Mar 2009, at 03:58, Buyean Lee wrote:
> 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
> >
> >
> >
> > A Good Credit Score is 700 or Above. See yours in just 2 easy steps!
>
> A Good Credit Score is 700 or Above. See yours in just 2 easy steps!
