Yingying,
Check the endianness of the file
/home/yingying/opt/fsl_feeds/data/fmri.nii.gz
if it is different than that of your machine then FSL with optimisations
has problems when byte swapping the header.
see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=FSL&P=R6273&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
I concur with Andrew, I have not found this problem in the precompiled
FSL versions since they tend to use nifticlib which doesnt have this
problem.
Chris.
On Fri, 2011-09-30 at 00:13 -0400, Yingying Wang wrote:
> Dear Matthew,
>
> Here is the message:
>
>
> Progress Report / Log
> Started at Thu Sep 29 01:13:48 EDT 2011
>
> Feat main script
>
>
> /bin/cp /home/yingying/opt/fsl_feeds/results/design.fsf design.fsf
>
> /home/yingying/opt/fsl_4_1_8/bin/feat_model design
>
> mkdir .files;cp /home/yingying/opt/fsl_4_1_8/doc/fsl.css .files;ln -s /home/yingying/opt/fsl_4_1_8/doc/images .files/images
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 18 -l logs -N feat2_pre -j featModelID /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -I 1 -prestats
> 13124
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 72 -l logs -N feat3_film -j 13124 /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -I 1 -film
> 13197
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 2 -l logs -N feat4_post -j 13197 /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -poststats 0 0
> 13239
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 13124 /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -I 1 -reg
> 13280
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 15 -l logs -N feat4_post -j 13239,13280 /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -poststats 1 0
> 13559
>
> /home/yingying/opt/fsl_4_1_8/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 13124,13197,13559,13280 /home/yingying/opt/fsl_4_1_8/bin/feat /home/yingying/opt/fsl_feeds/results/fmri.feat/design.fsf -D /home/yingying/opt/fsl_feeds/results/fmri.feat -stop
>
> ______________________________________________________________________
> Prestats
> /home/yingying/opt/fsl_4_1_8/bin/fslmaths /home/yingying/opt/fsl_feeds/data/fmri prefiltered_func_data -odt float
> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
> ** ERROR (nifti_image_read): cannot create nifti image from header '/home/yingying/opt/fsl_feeds/data/fmri.nii.gz'
> ** ERROR: nifti_image_open(/home/yingying/opt/fsl_feeds/data/fmri): bad header info
> ERROR: failed to open file /home/yingying/opt/fsl_feeds/data/fmri
> Cannot open volume /home/yingying/opt/fsl_feeds/data/fmri for reading!
> Total original volumes = 0
> Error - prefiltered_func_data has a different number of time points to that in FEAT setup
>
> ______________________________________________________________________
> Stats
> cat: absbrainthresh.txt: No such file or directory
> while executing
> "exec sh -c "cat absbrainthresh.txt" "
> (procedure "feat5:proc_film" line 57)
> invoked from within
> "feat5:proc_film $session "
> ("-film" 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/yingying/opt/fsl_4_1_8/bin/feat" line 137)
>
> ______________________________________________________________________
> Post-stats
> /home/yingying/opt/fsl_4_1_8/bin/contrast_mgr -f design.fts 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: Could not open image stats/sigmasquareds
> Image Exception : #22 :: Failed to read volume stats/sigmasquareds
>
>
> An exception has been thrown
> Failed to read volume stats/sigmasquaredsTrace: read_volume4DROI; ContrastMgr::Load; ContrastMgr::run.
>
> couldn't change working directory to "/home/yingying/opt/fsl_feeds/results/fmri.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 "/home/yingying/opt/fsl_4_1_8/bin/feat" line 137)
> couldn't change working directory to "/home/yingying/opt/fsl_feeds/results/fmri.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 "/home/yingying/opt/fsl_4_1_8/bin/feat" line 137)
>
> ______________________________________________________________________
> Registration
> /bin/mkdir -p reg
>
> /home/yingying/opt/fsl_4_1_8/bin/fslmaths /home/yingying/opt/fsl_feeds/data/structural_brain highres
> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
> ** ERROR (nifti_image_read): cannot create nifti image from header '/home/yingying/opt/fsl_feeds/data/structural_brain.nii.gz'
> ** ERROR: nifti_image_open(/home/yingying/opt/fsl_feeds/data/structural_brain): bad header info
> ERROR: failed to open file /home/yingying/opt/fsl_feeds/data/structural_brain
> Cannot open volume /home/yingying/opt/fsl_feeds/data/structural_brain for reading!
>
> /home/yingying/opt/fsl_4_1_8/bin/fslmaths /home/yingying/opt/fsl_4_1_8/data/standard/MNI152_T1_2mm_brain standard
>
> /home/yingying/opt/fsl_4_1_8/bin/flirt -ref highres -in example_func -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
> ** ERROR (nifti_image_read): failed to find header file for 'highres'
> ** ERROR: nifti_image_open(highres): bad header info
> ERROR: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> /home/yingying/opt/fsl_4_1_8/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
> Could not open matrix file example_func2highres.mat
> Cannot read input-matrix
>
> /home/yingying/opt/fsl_4_1_8/bin/slicer example_func2highres highres -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 ; /home/yingying/opt/fsl_4_1_8/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_func2highres1.png ; /home/yingying/opt/fsl_4_1_8/bin/slicer highres example_func2highres -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 ; /home/yingying/opt/fsl_4_1_8/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_func2highres2.png ; /home/yingying/opt/fsl_4_1_8/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png
> ** ERROR (nifti_image_read): failed to find header file for 'example_func2highres'
> ** ERROR: nifti_image_open(example_func2highres): bad header info
> ERROR: failed to open file example_func2highres
> ERROR: Could not open image example_func2highres
> Image Exception : #22 :: Failed to read volume example_func2highres
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> Cannot open sla.png for reading
> Segmentation fault
> ** ERROR (nifti_image_read): failed to find header file for 'highres'
> ** ERROR: nifti_image_open(highres): bad header info
> ERROR: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open example_func2highres1.png for reading
> Segmentation fault
>
> /home/yingying/opt/fsl_4_1_8/bin/flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
> ** ERROR (nifti_image_read): failed to find header file for 'highres'
> ** ERROR: nifti_image_open(highres): bad header info
> ERROR: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> /home/yingying/opt/fsl_4_1_8/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
> Could not open matrix file highres2standard.mat
> Cannot read input-matrix
>
> /home/yingying/opt/fsl_4_1_8/bin/slicer highres2standard 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 ; /home/yingying/opt/fsl_4_1_8/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 highres2standard1.png ; /home/yingying/opt/fsl_4_1_8/bin/slicer standard highres2standard -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 ; /home/yingying/opt/fsl_4_1_8/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 highres2standard2.png ; /home/yingying/opt/fsl_4_1_8/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png
> ** ERROR (nifti_image_read): failed to find header file for 'highres2standard'
> ** ERROR: nifti_image_open(highres2standard): bad header info
> ERROR: failed to open file highres2standard
> ERROR: Could not open image highres2standard
> Image Exception : #22 :: Failed to read volume highres2standard
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open highres2standard1.png for reading
> Segmentation fault
>
> /home/yingying/opt/fsl_4_1_8/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
> Could not open matrix file example_func2highres.mat
> Cannot read input-matrix
>
> /home/yingying/opt/fsl_4_1_8/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
> ** ERROR (nifti_image_read): failed to find header file for 'example_func'
> ** ERROR: nifti_image_open(example_func): bad header info
> ERROR: failed to open file example_func
> ERROR: Could not open image example_func
> Image Exception : #22 :: Failed to read volume example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> /home/yingying/opt/fsl_4_1_8/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
> Could not open matrix file example_func2standard.mat
> Cannot read input-matrix
>
> /home/yingying/opt/fsl_4_1_8/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 ; /home/yingying/opt/fsl_4_1_8/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 ; /home/yingying/opt/fsl_4_1_8/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 ; /home/yingying/opt/fsl_4_1_8/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 ; /home/yingying/opt/fsl_4_1_8/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png
> ** ERROR (nifti_image_read): failed to find header file for 'example_func2standard'
> ** ERROR: nifti_image_open(example_func2standard): bad header info
> ERROR: failed to open file example_func2standard
> ERROR: Could not open image example_func2standard
> Image Exception : #22 :: Failed to read volume example_func2standard
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open example_func2standard1.png for reading
> Segmentation fault
>
> Thanks.
> Yingying
>
>
>
> ==============================================
> Yingying Wang
> Graduate Student
> Biomedical Engineering
> University of Cincinnati
> Pediatric Neuroimaging Consortium Research Center
> Cincinnati Children's Hospital Medical Center
> MLC 5033, 3333 Burnet Avenue
> Cincinnati, OH 45229-3039
> O 513-636-3495
> C 513-833-7448
>
> >>> Matthew Webster 09/29/11 6:27 AM >>>
> Hello,
> If you check the log files in the generated
> results/fmri.feat directory, there should hopefully be more specific
> error-messages related to the FEAT test.
>
>
> Many Regards
>
>
> Matthew
>
>
> P.S.
> For debian/Ubuntu systems we recommend installing the precompiled FSL
> binaries from http://neuro.debian.net/pkgs/fsl.html
> > Dear FSL Team,
> >
> > I had feeds error (I compiled fsl 4.1.8 myself) :
> >
> > yingying@yingying-debian:~/opt/fsl_feeds$ ./RUN all
> >
> > FSL Evaluation and Example Data Suite v4.1.8
> >
> > start time = Wed Sep 28 23:30:34 EDT 2011
> > hostname = yingying-debian
> > os = Linux yingying-debian 2.6.32-5-amd64 #1 SMP Fri Sep 9 20:23:16
> > UTC 2011 x86_64 GNU/Linux
> >
> >
> > /bin/rm -rf /home/yingying/opt/fsl_feeds/results ;
> > mkdir /home/yingying/opt/fsl_feeds/results
> >
> >
> > Starting PRELUDE & FUGUE at Wed Sep 28 23:30:34 EDT 2011
> > % error = 0.0
> > % error = 0.0
> >
> > Starting SUSAN at Wed Sep 28 23:30:35 EDT 2011
> > % error = 0.03
> >
> > Starting SIENAX (including testing BET and FLIRT and FAST) at Wed
> > Sep 28 23:32:22 EDT 2011
> > checking error on BET:
> > % error = 0.0
> > checking error on FLIRT:
> > % error = 0.0
> > checking error on FAST:
> > checking error on single-image binary segmentation:
> > % error = 0.37
> > checking error on partial volume images:
> > % error = 0.28
> > % error = 0.41
> > % error = 0.29
> > checking error on SIENAX volume outputs:
> > % error = 0.18
> > % error = 0.11
> > % error = 0.49
> > % error = 0.02
> > % error = 0.51
> >
> > Starting BET2 at Wed Sep 28 23:45:15 EDT 2011
> > checking error on T1 brain extraction:
> > % error = 0.0
> > checking error on skull and scalp surfaces:
> > % error = 0.02
> > % error = 0.03
> > % error = 0.14
> >
> > Starting FEAT at Wed Sep 28 23:53:08 EDT 2011
> > checking error on filtered functional data:
> > No output image created
> > Warning - test failed!
> > checking error on raw Z stat images:
> > No output image created
> > Warning - test failed!
> > No output image created
> > Warning - test failed!
> > No output image created
> > Warning - test failed!
> > checking error on thresholded Z stat images:
> > No output image created
> > Warning - test failed!
> > No output image created
> > Warning - test failed!
> > No output image created
> > Warning - test failed!
> > checking error on registration images:
> > No output image created
> > Warning - test failed!
> > No output image created
> > Warning - test failed!
> > checking error on position of largest cluster of Talairached
> > zfstat1:
> > couldn't open
> > "/home/yingying/opt/fsl_feeds/results/fmri.feat/cluster_zfstat1_std.txt": no such file or directory
> > while executing
> > "open ${FEEDSDIR}/results/fmri.feat/cluster_zfstat1_std.txt r "
> > invoked from within
> > "if { $feeds(feat) } {
> >
> > puts "\nStarting FEAT at [ exec date ]"
> >
> > # fix FEAT setup file to use FEEDSDIR and FSLDIR
> > fsl:exec "cp ${FEEDSDIR}/data/fmri.fe..."
> > (file "./RUN" line 285)
> >
> > Why FEAT will not work?
> >
> > Thanks a lot.
> > yingying
> >
>
>
>
> ______________________________________________________________________
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>
> If you have any question, please contact MCRI IT Helpdesk for further
> assistance.
> ______________________________________________________________________
--
Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons.,
Monash)
Research Officer
Developmental Imaging, Critical Care and Neurosciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road Parkville Victoria 3052 Australia
T 9345 4306
M XXXX XXX XXX
E [log in to unmask]
www.mcri.edu.au
______________________________________________________________________
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