Dear Kristina,
This is very odd.
It looks like your fslcreatehd is broken.
Which binary package did you download?
All the best,
Mark
On 8 Jun 2012, at 19:43, Kristina Skatun wrote:
> Dear Mark,
>
> Thank you for your input! Unfortunately, the problem is still not resolved...
>
> The tmpHeader file was correctly altered (so that the dt = '3.0') by changing to
> fmri/av% /home/software/fsl/bin/fslhd -x filtered_func_data | sed "s/ dt = .*/ dt = \'3.0\'/g" > tmpHeader
>
> tmpHeader:
>
> <nifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = 'filtered_func_data.nii.gz'
> image_filename = 'filtered_func_data.nii.gz'
> image_offset = '352'
> ndim = '4'
> nx = '64'
> ny = '64'
> nz = '5'
> nt = '45'
> dx = '4'
> dy = '4'
> dz = '6'
> dt = '3.0'
> datatype = '16'
> datatype_name = 'FLOAT32'
> nvox = '921600'
> nbyper = '4'
> byteorder = 'LSB_FIRST'
> scl_slope = '1'
> scl_inter = '0'
> xyz_units = '2'
> xyz_units_name = 'mm'
> time_units = '8'
> time_units_name = 's'
> descrip = 'FSL4.1'
> qform_code = '1'
> qform_code_name = 'Scanner Anat'
> qto_xyz_matrix = '-4 0 -0 0 0 4 -0 0 0 0 6 0 0 0 0 1'
> qto_ijk_matrix = '-0.25 0 -0 -0 0 0.25 0 -0 -0 -0 0.166667 -0 0 0 0 1'
> quatern_b = '0'
> quatern_c = '1'
> quatern_d = '0'
> qoffset_x = '0'
> qoffset_y = '0'
> qoffset_z = '0'
> qfac = '-1'
> qform_i_orientation = 'Right-to-Left'
> qform_j_orientation = 'Posterior-to-Anterior'
> qform_k_orientation = 'Inferior-to-Superior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '-4 0 0 0 0 4 0 0 0 0 6 0 0 0 0 1'
> sto_ijk matrix = '-0.25 -0 -0 -0 -0 0.25 -0 -0 -0 -0 0.166667 -0 0 0 0 1'
> sform_i_orientation = 'Right-to-Left'
> sform_j_orientation = 'Posterior-to-Anterior'
> sform_k_orientation = 'Inferior-to-Superior'
> num_ext = '0'
> />
>
> However, the same error persisted in the following step (fslcreatehd):
>
> ------------------------------------------------------------------
> fmri/av% /home/software/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
> fmri/av% /home/software/fsl/bin/fslhd -x filtered_func_data | sed "s/ dt = .*/ dt = \'3.0\'/g" > tmpHeader
> fmri/av% /home/software/fsl/bin/fslcreatehd tmpHeader filtered_func_data
> Incomplete or incorrect text: could not form header info
> *** glibc detected *** /home/software/fsl/bin/fslcreatehd: free(): invalid pointer: 0x000000000059ad20 ***
> ======= Backtrace: =========
> /lib64/libc.so.6(+0x74c06)[0x7f7391145c06]
> /usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE26_M_destroy_internal_bufferEv+0x1e)[0x7f73919499fe]
> /usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE5closeEv+0x4e)[0x7f739194a64e]
> /home/software/fsl/bin/fslcreatehd[0x402cef]
> /home/software/fsl/bin/fslcreatehd[0x402e75]
> /lib64/libc.so.6(__libc_start_main+0xed)[0x7f73910f223d]
> /home/software/fsl/bin/fslcreatehd(__gxx_personality_v0+0x6a)[0x40219a]
> ======= Memory map: ========
> 00400000-0043b000 r-xp 00000000 08:03 4980928 /home/software/fsl/bin/fslcreatehd
> 0053b000-0053c000 rw-p 0003b000 08:03 4980928 /home/software/fsl/bin/fslcreatehd
> 0053c000-005bb000 rw-p 00000000 00:00 0 [heap]
> 7f7390d4c000-7f73910d1000 rw-p 00000000 00:00 0
> 7f73910d1000-7f7391256000 r-xp 00000000 08:02 1183138 /lib64/libc-2.14.1.so
> 7f7391256000-7f7391456000 ---p 00185000 08:02 1183138 /lib64/libc-2.14.1.so
> 7f7391456000-7f739145a000 r--p 00185000 08:02 1183138 /lib64/libc-2.14.1.so
> 7f739145a000-7f739145b000 rw-p 00189000 08:02 1183138 /lib64/libc-2.14.1.so
> 7f739145b000-7f7391460000 rw-p 00000000 00:00 0
> 7f7391460000-7f7391475000 r-xp 00000000 08:02 1183136 /lib64/libgcc_s.so.1
> 7f7391475000-7f7391674000 ---p 00015000 08:02 1183136 /lib64/libgcc_s.so.1
> 7f7391674000-7f7391675000 r--p 00014000 08:02 1183136 /lib64/libgcc_s.so.1
> 7f7391675000-7f7391676000 rw-p 00015000 08:02 1183136 /lib64/libgcc_s.so.1
> 7f7391676000-7f73916cc000 r-xp 00000000 08:02 1182986 /lib64/libm-2.14.1.so
> 7f73916cc000-7f73918cb000 ---p 00056000 08:02 1182986 /lib64/libm-2.14.1.so
> 7f73918cb000-7f73918cc000 r--p 00055000 08:02 1182986 /lib64/libm-2.14.1.so
> 7f73918cc000-7f73918cd000 rw-p 00056000 08:02 1182986 /lib64/libm-2.14.1.so
> 7f73918cd000-7f73919b9000 r-xp 00000000 08:02 1059528 /usr/lib64/libstdc++.so.6.0.16
> 7f73919b9000-7f7391bb8000 ---p 000ec000 08:02 1059528 /usr/lib64/libstdc++.so.6.0.16
> 7f7391bb8000-7f7391bc0000 r--p 000eb000 08:02 1059528 /usr/lib64/libstdc++.so.6.0.16
> 7f7391bc0000-7f7391bc2000 rw-p 000f3000 08:02 1059528 /usr/lib64/libstdc++.so.6.0.16
> 7f7391bc2000-7f7391bd7000 rw-p 00000000 00:00 0
> 7f7391bd7000-7f7391bf7000 r-xp 00000000 08:02 1183009 /lib64/ld-2.14.1.so
> 7f7391dd2000-7f7391dd8000 rw-p 00000000 00:00 0
> 7f7391df4000-7f7391df7000 rw-p 00000000 00:00 0
> 7f7391df7000-7f7391df8000 r--p 00020000 08:02 1183009 /lib64/ld-2.14.1.so
> 7f7391df8000-7f7391df9000 rw-p 00021000 08:02 1183009 /lib64/ld-2.14.1.so
> 7f7391df9000-7f7391dfa000 rw-p 00000000 00:00 0
> 7fff6d507000-7fff6d529000 rw-p 00000000 00:00 0 [stack]
> 7fff6d5ff000-7fff6d600000 r-xp 00000000 00:00 0 [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
> Abort
>
>
> ------------------------------------------------------------------
>
> Do you have any other idea what might be wrong? Again, thanks a lot for you help!
>
> Regards,
> -Kristina
>
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