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It works after removing the nan values.
Thanks a million!

Buyean Lee


-----Original Message-----
From: Mark Jenkinson <[log in to unmask]>
To: [log in to unmask]
Sent: Tue, 3 Mar 2009 12:38 am
Subject: Re: [FSL] first_flirt error

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 
> > 
> > 
> > 
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