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FSL  June 2012

FSL June 2012

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Subject:

Re: error "glibc detected" in prestats

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 6 Jun 2012 12:00:06 +0930

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (139 lines)

Dear Kristina,

I think the problem may be coming from the line:
> /home/software/fsl/bin/fslhd -x filtered_func_data | sed 's/  dt = .*/ dt = '3.0'/g' > tmpHeader
in that it is not producing correct output.

Can you send us the contents of the file tmpHeader (from your command line run)?

It can hopefully be fixed easily if we can see what is going on.

All the best,
	Mark




On 4 Jun 2012, at 16:55, Kristina Skatun wrote:

> Hi everyone,
> 
> I'm in the process of learning fsl, and have been working through the course data available at the fsl website. However, when trying to run MELODIC or FEAT from the gui i get an error in the prestats section. The same problem persists both with the fsl course data and with own data. The prestats web log is as follows:
> 
> ------------------------------------------------------------------
> Prestats
> 
> /home/software/fsl/bin/fslmaths /home/fmri/Data/Test_kristina/FSL/fsl_course_data/fmri/av/fmri prefiltered_func_data -odt float
> Total original volumes = 45
> 
> /home/software/fsl/bin/fslroi prefiltered_func_data example_func 22 1
> 
> /home/software/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 22 -rmsrel -rmsabs
> 
> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
> 
> /home/software/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png
> 
> /home/software/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png
> 
> /home/software/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png
> 
> /home/software/fsl/bin/fslstats prefiltered_func_data_mcf -p 2 -p 98
> 0.000000 9918.897461
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_mcf -thr 991.8897461 -Tmin -bin mask -odt char
> 
> /home/software/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
> 7351.893555
> 
> /home/software/fsl/bin/fslmaths mask -dilF mask
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
> 
> /home/software/fsl/bin/susan prefiltered_func_data_thresh 5513.92016625 2.12314225053 3 1 1 mean_func 5513.92016625 prefiltered_func_data_smooth
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 1.36019379568 prefiltered_func_data_intnorm
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 16.6666666667 -1 prefiltered_func_data_tempfilt
> 
> /home/software/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
> 
> /home/software/fsl/bin/fslhd -x filtered_func_data | sed 's/  dt = .*/ dt = '3.0'/g' > tmpHeader
> 
> /home/software/fsl/bin/fslcreatehd tmpHeader filtered_func_data
> Incomplete or incorrect text: could not form header info
> 
> /bin/rm tmpHeader
> 
> /home/software/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
> ** ERROR (nifti_image_read): short header read 'filtered_func_data.nii.gz'
> ** ERROR: nifti_image_open(filtered_func_data): bad header info
> ERROR: failed to open file filtered_func_data
> Cannot open volume filtered_func_data for reading!
> 
> /bin/rm -rf prefiltered_func_data*
> 
> ------------------------------------------------------------------
> 
> When I ran each step separately via the terminal, i got this error when attempting to run the fslcreatehd:
> 
> 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)[0x7ff980c3cc06]
> /usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE26_M_destroy_internal_bufferEv+0x1e)[0x7ff9814409fe]
> /usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE5closeEv+0x4e)[0x7ff98144164e]
> /home/software/fsl/bin/fslcreatehd[0x402cef]
> /home/software/fsl/bin/fslcreatehd[0x402e75]
> /lib64/libc.so.6(__libc_start_main+0xed)[0x7ff980be923d]
> /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]
> 7ff980843000-7ff980bc8000 rw-p 00000000 00:00 0
> 7ff980bc8000-7ff980d4d000 r-xp 00000000 08:02 1183138  /lib64/libc-2.14.1.so
> 7ff980d4d000-7ff980f4d000 ---p 00185000 08:02 1183138  /lib64/libc-2.14.1.so
> 7ff980f4d000-7ff980f51000 r--p 00185000 08:02 1183138  /lib64/libc-2.14.1.so
> 7ff980f51000-7ff980f52000 rw-p 00189000 08:02 1183138  /lib64/libc-2.14.1.so
> 7ff980f52000-7ff980f57000 rw-p 00000000 00:00 0
> 7ff980f57000-7ff980f6c000 r-xp 00000000 08:02 1183136  /lib64/libgcc_s.so.1
> 7ff980f6c000-7ff98116b000 ---p 00015000 08:02 1183136  /lib64/libgcc_s.so.1
> 7ff98116b000-7ff98116c000 r--p 00014000 08:02 1183136  /lib64/libgcc_s.so.1
> 7ff98116c000-7ff98116d000 rw-p 00015000 08:02 1183136  /lib64/libgcc_s.so.1
> 7ff98116d000-7ff9811c3000 r-xp 00000000 08:02 1182986  /lib64/libm-2.14.1.so
> 7ff9811c3000-7ff9813c2000 ---p 00056000 08:02 1182986  /lib64/libm-2.14.1.so
> 7ff9813c2000-7ff9813c3000 r--p 00055000 08:02 1182986  /lib64/libm-2.14.1.so
> 7ff9813c3000-7ff9813c4000 rw-p 00056000 08:02 1182986  /lib64/libm-2.14.1.so
> 7ff9813c4000-7ff9814b0000 r-xp 00000000 08:02 1059528  /usr/lib64/libstdc++.so.6.0.16
> 7ff9814b0000-7ff9816af000 ---p 000ec000 08:02 1059528  /usr/lib64/libstdc++.so.6.0.16
> 7ff9816af000-7ff9816b7000 r--p 000eb000 08:02 1059528  /usr/lib64/libstdc++.so.6.0.16
> 7ff9816b7000-7ff9816b9000 rw-p 000f3000 08:02 1059528  /usr/lib64/libstdc++.so.6.0.16
> 7ff9816b9000-7ff9816ce000 rw-p 00000000 00:00 0
> 7ff9816ce000-7ff9816ee000 r-xp 00000000 08:02 1183009  /lib64/ld-2.14.1.so
> 7ff9818c9000-7ff9818cf000 rw-p 00000000 00:00 0
> 7ff9818eb000-7ff9818ee000 rw-p 00000000 00:00 0
> 7ff9818ee000-7ff9818ef000 r--p 00020000 08:02 1183009  /lib64/ld-2.14.1.so
> 7ff9818ef000-7ff9818f0000 rw-p 00021000 08:02 1183009  /lib64/ld-2.14.1.so
> 7ff9818f0000-7ff9818f1000 rw-p 00000000 00:00 0
> 7fffd965c000-7fffd967e000 rw-p 00000000 00:00 0  [stack]
> 7fffd97ff000-7fffd9800000 r-xp 00000000 00:00 0  [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0  [vsyscall]
> Abort
> fmri/av%
> 
> ------------------------------------------------------------------
> 
> The filtered_func_data file is fine and can opened in fslview before "fslcreatehd tmpHeader filtered_func_data" is run, after that it can no longer be opened. Any suggestions how to fix this problem? I had no problem when i ran the same data on my windows VM so seems there is something specific to the linux (OS: OpenSuse 12.1, 64-bit memory).
> 
> Any input would be much appreciated!
> 
> Regards,
> 
> -Kristina
> 

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