Hi,
Until we release a fixed version of fslstats, the only thing to
try is running the analysis on a machine with more RAM...
Matt
> 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)
