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