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
|