Thanks for your message! What should I do about fixing the problem?
Best wishes,
Rebecca
Rebecca Chandler
University of Oxford Department of Psychiatry
Warneford Hospital
Oxford
OX3 7JX
Tel: +44 1865 223790
Fax: +44 1865 793101
Email: [log in to unmask]
>>> Matthew Webster <[log in to unmask]> 11/9/2007 1:44 PM >>>
Hi,
We're currently seeing a bug for some runs where the input has
more than ~600 volumes (specifically this is a fslstats problem) -
we're still investigating how to fix this.
many regards
Matthew
> Hello,
> I keep getting the following error message when I try and run a
> stats and
> poststats FEAT. Can you please help me figure what it means and
> what I can
> do to fix the problem? I have previously run FEATS using the same
> brains
> successfully.
>
> Thanks for your help!
>
> Prestats
>
> Total original volumes = 729
>
> /Users/rebeccachandler/fsl/bin/fslroi
> /Volumes/G-DRIVE/MR_cxr/subject1/1st_level_cxr_NoUnwarp.feat/
> denoised_data
> example_func 364 1
>
> /Users/rebeccachandler/fsl/bin/fslmaths
> /Volumes/G-DRIVE/MR_cxr/subject1/1st_level_cxr_NoUnwarp.feat/
> denoised_data
> filtered_func_data
>
> /Users/rebeccachandler/fsl/bin/fslmaths filtered_func_data -Tmin -
> bin mask
> -odt char
>
> /Users/rebeccachandler/fsl/bin/fslstats filtered_func_data -k mask -
> R | awk
> '{ print }' -
> fslstats(2686) malloc: *** vm_allocate(size=737280) failed (error
> code=3)
> fslstats(2686) malloc: *** error: can't allocate region
> fslstats(2686) malloc: *** set a breakpoint in szone_error to debug
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
>
> /Users/rebeccachandler/fsl/bin/fslmaths filtered_func_data -Tmean
> mean_func
>
> /bin/rm -rf prefiltered_func_data*
>
> Stats
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t1.ev
> custom_timing_files/ev1.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t2.ev
> custom_timing_files/ev2.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t3.ev
> custom_timing_files/ev3.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t4.ev
> custom_timing_files/ev4.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t5.ev
> custom_timing_files/ev5.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t6.ev
> custom_timing_files/ev6.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t7.ev
> custom_timing_files/ev7.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t8.ev
> custom_timing_files/ev8.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t9.ev
> custom_timing_files/ev9.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_t10.ev
> custom_timing_files/ev10.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_wins.ev
> custom_timing_files/ev11.txt
>
> mkdir -p custom_timing_files ; /bin/cp
> /Volumes/G-DRIVE/MR_cxr/EV/cxr_ev/subject1_cxr/subject1_losses.ev
> custom_timing_files/ev12.txt
>
> /Users/rebeccachandler/fsl/bin/film_gls -rn stats -sa -ms 5 -sp
> /Users/rebeccachandler/fsl/bin/susan_smooth filtered_func_data
> design.mat
> what(): St9bad_alloc
> sh: -c: line 1: syntax error near unexpected token `('
> sh: -c: line 1: `/Users/rebeccachandler/fsl/bin/film_gls -rn stats -
> sa -ms 5
> -sp /Users/rebeccachandler/fsl/bin/susan_smooth filtered_func_data
> design.mat what(): St9bad_alloc'
> Error: FILM did not complete - it probably ran out of memory
>
> Post-stats
>
> /Users/rebeccachandler/fsl/bin/contrast_mgr stats design.con
> ** ERROR (nifti_image_read): failed to find header file for
> 'stats/sigmasquareds'
> ** ERROR: nifti_image_open(stats/sigmasquareds): bad header info
> Error: failed to open file stats/sigmasquareds
> Error:: FslGetDim: Null pointer passed for FSLIO
> couldn't change working directory to
> "/Volumes/G-DRIVE/MR_cxr/subject1/2nd_level_cxr_NoUnwarp.feat/
> stats": no
> such file or directory
> while executing
> "cd ${FD}/stats"
> (procedure "feat5:proc_poststats" line 50)
> invoked from within
> "feat5:proc_poststats $RERUNNING $STDSPACE "
> ("-poststats" arm line 6)
> invoked from within
> "switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set session [ lindex $argv $argindex ]
> }
>
> -D {
> incr argindex 1
> set..."
> ("for" body line 2)
> invoked from within
> "for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set ses..."
> (file "/Users/rebeccachandler/fsl/bin/feat" line 137)
> couldn't change working directory to
> "/Volumes/G-DRIVE/MR_cxr/subject1/2nd_level_cxr_NoUnwarp.feat/
> stats": no
> such file or directory
> while executing
> "cd ${FD}/stats"
> (procedure "feat5:proc_poststats" line 50)
> invoked from within
> "feat5:proc_poststats $RERUNNING $STDSPACE "
> ("-poststats" arm line 6)
> invoked from within
> "switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set session [ lindex $argv $argindex ]
> }
>
> -D {
> incr argindex 1
> set..."
> ("for" body line 2)
> invoked from within
> "for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set ses..."
> (file "/Users/rebeccachandler/fsl/bin/feat" line 137)
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