Hi,
Have you tried cutting down your image in space to just a few slices in order to see if that works?
For instance, you could try a 4 slice version (from the centre) by running:
fslroi orig_data cutdown_data 0 96 0 96 24 4 0 640
If this worked fine then it would be an indication that you truly have a memory problem and could try different numbers of slices to see how big you could make the images for your machine.
Oh, and if you have 12GB of RAM, you should have at least 20GB of swap.
All the best,
Mark
On 23 Dec 2010, at 14:52, Habib ganjgahi wrote:
> Hi, I tried many times but the error still exist also the swap space was increased to 10 GB,
> Unfortunately that didn't work. Is there any solution?
>
>
> On Wed, Dec 22, 2010 at 4:45 PM, Stephen Smith <[log in to unmask]> wrote:
> Hi - this all looks fine up until the crash - so it looks like maybe you did run out of RAM/swap - maybe lots of other processes were running on your computer at the same time. Do you have plenty of swap? I suggest trying running again from the start.
>
> Cheers.
>
>
>
> On 22 Dec 2010, at 09:36, Habib ganjgahi wrote:
>
>> Dear Steve
>>
>> Hi, I ran the commands and you can find the outputs.
>> What is your suggestion?
>>
>> Best,
>> Habib
>>
>> On Wed, Dec 22, 2010 at 11:44 AM, Stephen Smith <[log in to unmask]> wrote:
>> Hi - hopefully this isn't a RAM problem, unless maybe your resolution is very high. Can you run the following and see what the output says:
>>
>> cd <into FEAT output directory>
>> ls -lrt
>> -rw-r--r-- 1 fsl fsl 7735 2010-12-21 09:53 design.fsf
>> -rw-r--r-- 1 fsl fsl 4 2010-12-21 09:53 design.frf
>> -rw-r--r-- 1 fsl fsl 852 2010-12-21 09:53 design.trg
>> -rw-r--r-- 1 fsl fsl 18065 2010-12-21 09:53 design.mat
>> -rw-r--r-- 1 fsl fsl 128 2010-12-21 09:53 design.con
>> -rw-r--r-- 1 fsl fsl 97410 2010-12-21 09:53 design_cov.ppm
>> -rw-r--r-- 1 fsl fsl 967 2010-12-21 09:53 design_cov.png
>> -rw-r--r-- 1 fsl fsl 317184 2010-12-21 09:53 design.ppm
>> -rw-r--r-- 1 fsl fsl 5967 2010-12-21 09:53 design.png
>> -rw-r--r-- 1 fsl fsl 166 2010-12-21 09:53 report_stats.html
>> -rw-r--r-- 1 fsl fsl 173 2010-12-21 09:53 report_reg.html
>> -rw-r--r-- 1 fsl fsl 170 2010-12-21 09:53 report_poststats.html
>> -rw-r--r-- 1 fsl fsl 412559878 2010-12-21 09:59 prefiltered_func_data.nii.gz
>> -rw-r--r-- 1 fsl fsl 644633 2010-12-21 10:00 example_func.nii.gz
>> -rw-r--r-- 1 fsl fsl 933000628 2010-12-21 10:08 prefiltered_func_data_mcf.nii.gz
>> drwxr-xr-x 3 fsl fsl 4096 2010-12-21 10:08 mc
>> -rw-r--r-- 1 fsl fsl 442 2010-12-21 10:08 report_prestats.html
>> -rw-r--r-- 1 fsl fsl 940391481 2010-12-21 10:35 prefiltered_func_data_st.nii.gz
>> -rw-r--r-- 1 fsl fsl 1469084 2010-12-21 10:35 mean_func.nii.gz
>> -rw-r--r-- 1 fsl fsl 8230 2010-12-21 10:35 mask.nii.gz
>> -rw-r--r-- 1 fsl fsl 263855240 2010-12-21 10:37 prefiltered_func_data_bet.nii.gz
>> drwxr-xr-x 2 fsl fsl 4096 2010-12-21 10:37 logs
>> -rw-r--r-- 1 fsl fsl 922 2010-12-21 10:37 report.html
>> -rw-r--r-- 1 fsl fsl 3339 2010-12-21 10:37 report_log.html
>>
>> fslstats prefiltered_func_data_bet -r -R
>> -2.024899 1214.941040 -27.116980 2482.091064
>>
>> fslhd prefiltered_func_data_bet
>> sizeof_hdr 348
>> data_type FLOAT32
>> dim0 4
>> dim1 96
>> dim2 96
>> dim3 49
>> dim4 640
>> dim5 1
>> dim6 1
>> dim7 1
>> vox_units mm
>> time_units s
>> datatype 16
>> nbyper 4
>> bitpix 32
>> pixdim0 0.0000000000
>> pixdim1 2.2916667461
>> pixdim2 2.2916667461
>> pixdim3 3.0000000000
>> pixdim4 1.0000000000
>> pixdim5 0.0000000000
>> pixdim6 0.0000000000
>> pixdim7 0.0000000000
>> vox_offset 352
>> cal_max 2482.0911
>> cal_min -27.1170
>> scl_slope 1.000000
>> scl_inter 0.000000
>> phase_dim 0
>> freq_dim 0
>> slice_dim 0
>> slice_name Unknown
>> slice_code 0
>> slice_start 0
>> slice_end 0
>> slice_duration 0.000000
>> time_offset 0.000000
>> intent Unknown
>> intent_code 0
>> intent_name
>> intent_p1 0.000000
>> intent_p2 0.000000
>> intent_p3 0.000000
>> qform_name Unknown
>> qform_code 0
>> qto_xyz:1 2.291667 0.000000 0.000000 0.000000
>> qto_xyz:2 0.000000 2.291667 0.000000 0.000000
>> qto_xyz:3 0.000000 0.000000 3.000000 0.000000
>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> qform_xorient Left-to-Right
>> qform_yorient Posterior-to-Anterior
>> qform_zorient Inferior-to-Superior
>> sform_name Unknown
>> sform_code 0
>> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:4 0.000000 0.000000 0.000000 0.000000
>> sform_xorient Unknown
>> sform_yorient Unknown
>> sform_zorient Unknown
>> file_type NIFTI-1+
>> file_code 1
>> descrip FSL4.0
>> aux_file
>>
>>
>> Cheers.
>>
>>
>> On 21 Dec 2010, at 17:12, Habib ganjgahi wrote:
>>
>>> Dear fsl experts
>>> Hi
>>>
>>> I want to analyze fmri data with 640 volumes but in pre stat stage, after motion correction an error was appeared.
>>> I searched the archive and realized that this error maybe due to Memory shortage but the data
>>> was analyzed in machine with 12 GB RAM, 64 bit cpu and compatible fsl version with 64-bit cpu (Ubuntu 10.4, 64 bit).
>>> Can I ask you to check the log file and have your solution?
>>>
>>> Thanks in advance
>>>
>>> Best Regards,
>>> Habib
>>>
>>>
>>> Prestats
>>>
>>> /home/fsl/fsl/bin/fslmaths /home/fsl/Functional/lie_
>>> detection/002/epi prefiltered_func_data -odt float
>>> Total original volumes = 640
>>>
>>> /home/fsl/fsl/bin/fslroi prefiltered_func_data example_func 320 1
>>>
>>> /home/fsl/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 320 -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/fsl/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/fsl/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/fsl/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/fsl/fsl/bin/slicetimer -i prefiltered_func_data_mcf --out=prefiltered_func_data_st -r 3.0
>>>
>>> /home/fsl/fsl/bin/fslmaths prefiltered_func_data_st -Tmean mean_func
>>>
>>> /home/fsl/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /home/fsl/fsl/bin/immv mask_mask mask
>>>
>>> /home/fsl/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_bet
>>>
>>> /home/fsl/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
>>> std::bad_alloc
>>> syntax error in expression "std::bad_alloc + ( 10 * ( - std::bad_alloc ) / 100.0 )": variable references require preceding $
>>> while executing
>>> "expr $int2 + ( $fmri(brain_thresh) * ( $int98 - $int2 ) / 100.0 ) "
>>> (procedure "feat5:proc_prestats" line 371)
>>> invoked from within
>>> "feat5:proc_prestats $session "
>>> ("-prestats" arm line 2)
>>> 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 "/home/fsl/fsl/bin/feat" line 137)
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>>
>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
|
