Hello,
Is there something unusual about your data? - the median intensity of the masked data is 0. I would start by looking at prefiltered_func_data_bet, prefiltered_func_data_st, prefiltered_func_data_thresh, and the mask image to see if anything looks odd.
Also can you confirm you are using the latest version of FSL ( 5.0.8 )?
Kind Regards
Matthew
<snip>
/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1261.354858
/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 126.1354858 -Tmin -bin mask -odt char
/usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
0.000000
<snip>
> Hi
>
> I have trouble with feat analysis for preprocessing fMRI data..
> I have used it for 2 years and I've got this error for the first time...
>
> I run 500 data and almost 100 data generate this error..
> I checked fMRI raw data and I run FEAT analysis only for error data but I've got same results..
>
> This is the list of feat folder
>
> design.con example_func.nii.gz reg
> design_cov.png logs report.html
> design_cov.ppm mask.nii.gz report_log.html
> design.frf mc report_poststats.html
> design.fsf mean_func.nii.gz report_prestats.html
> design.mat prefiltered_func_data_bet.nii.gz report_reg.html
> design.min prefiltered_func_data_mcf.nii.gz report_stats.html
> design.png prefiltered_func_data.nii.gz report_unwarp.html
> design.ppm prefiltered_func_data_st.nii.gz
> design.trg prefiltered_func_data_thresh.nii.gz
>
> Any advise would be very much appreciated..
>
> Thank you!
>
> --------------------------------------------------------------------------------------------
> Progress Report / Log
> Started at Mon Aug 17 11:27:31 KST 2015
>
> Feat main script
>
>
> /bin/cp /tmp/feat_lmuEwF.fsf design.fsf
>
> /usr/local/fsl/bin/feat_model design
>
> mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s /usr/local/fsl/doc/images .files/images
>
> /usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -I 1 -init
> 18309
>
> /usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat1b_reg -j 18309 /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -I 1 -reg
> 18493
>
> /usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat2_pre -j 18493,18309 /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -I 1 -prestats
> divide by zero
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 55 -l logs -N feat3_film /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -I 1 -film
> cat: absbrainthresh.txt: No such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat4_post /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -poststats 0 0
> couldn't change working directory to "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/stats": no such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 18493 /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -poststats 1 0
> couldn't change working directory to "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/stats": no such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> /usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 18493 /usr/local/fsl/bin/feat /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/design.fsf -D /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -stop
>
> ------------------------------------------------------------------------------------------------------------------------------------
> Initialisation
>
>
> /usr/local/fsl/bin/fslmaths /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri prefiltered_func_data -odt float
> Total original volumes = 100
> Deleting 3 volume(s) - BE WARNED for future analysis!
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 3 97
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 48 1
>
> /usr/local/fsl/bin/mainfeatreg -d /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat -l /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/logs/feat5_reg -R /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/report_unwarp.html -r /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/report_reg.html -i /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/example_func.nii.gz -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
> Option -d ( output directory ) selected with argument "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat"
> Option -l ( logfile )input with argument "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/logs/feat5_reg"
> Option -R ( html unwarping report ) selected with argument "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with argument "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/report_reg.html"
> Option -i ( main input ) input with argument "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/example_func.nii.gz"
> Option -s ( standard image ) selected with argument "/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"
> Option -y ( standard dof ) selected with argument "12"
> Option -z ( standard search ) selected with argument "90"
>
>
> ------------------------------------------------------------------------------------------------------------------------------------
> Prestats
>
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -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
>
> /usr/local/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
>
> /usr/local/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
>
> /usr/local/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
>
> /usr/local/fsl/bin/slicetimer -i prefiltered_func_data_mcf --out=prefiltered_func_data_st -r 3.0000000000 --down
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -Tmean mean_func
>
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv mask_mask mask
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_bet
>
> /usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
> 0.000000 1261.354858
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 126.1354858 -Tmin -bin mask -odt char
>
> /usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
> 0.000000
>
> /usr/local/fsl/bin/fslmaths mask -dilF mask
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_thresh
> divide by zero
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> Stats
>
> cat: absbrainthresh.txt: No such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
> ------------------------------------------------------------------------------------------------------------------------------
> Post-stats
>
>
> /usr/local/fsl/bin/contrast_mgr stats design.con
> Image Exception : #22 :: ERROR: Could not open image stats/sigmasquareds
>
>
> An exception has been thrown
> ERROR: Could not open image stats/sigmasquaredsTrace: read_volume4DROI; ContrastMgr::Load; ContrastMgr::run.
>
> couldn't change working directory to "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/stats": no such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
> couldn't change working directory to "/home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/stats": no such file or directory
> while executing
> "if { [ catch {
>
>
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argin..."
> (file "/usr/local/fsl/bin/feat" line 119)
>
>
> ------------------------------------------------------------------------------------------------------------------------------------
> Registration
>
>
> /bin/mkdir -p /home/hyo/Desktop/AAL/1928_data/fmri/nii/00131734_110814_fmri.feat/reg
>
>
> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard
>
> did not find file: example_func2standard.mat. Generating transform.
>
> /usr/local/fsl/bin/flirt -in example_func -ref standard -out example_func2standard -omat example_func2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>
>
> /usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
>
>
> /usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
>
>
|