Friday, September 30, 2011

FSL FEEDS error work around.

Good news:  I did try to work around this.

See the following command.  I 3dcopy the original fmri.nii.gz

yingying@yingying-debian:~/opt/fsl_feeds/data$ 3dcopy fmri.nii.gz fmri_afni.nii.gz
++ 3dcopy: AFNI version=AFNI_2011_05_26_1457 (Aug 19 2011) [64-bit]
*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file 'fmri.nii.gz'

yingying@yingying-debian:~/opt/fsl_feeds/data$ /home/yingying/opt/fsl_4_1_8/bin/melodic -i /home/yingying/opt/fsl_feeds/data/fmri_afni -o /home/yingying/opt/fsl_feeds/results/fmri.ica --tr=3 --seed=2

Then, it works.  Error messages are gone.

This question still puzzles me.  Any comments are welcome.

>>> Yingying Wang 09/30/11 11:07 PM >>>
/home/yingying/opt/fsl_4_1_8/bin/melodic -i /home/yingying/opt/fsl_feeds/data/fmri -o /home/yingying/opt/fsl_feeds/results/fmri.ica --tr=3 --seed=2
** 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
ERROR: Could not open image /home/yingying/opt/fsl_feeds/data/fmri
Image Exception : #22 :: Failed to read volume /home/yingying/opt/fsl_feeds/data/fmri



An exception has been thrown
Failed to read volume /home/yingying/opt/fsl_feeds/data/fmriTrace: read_volumeROI.


/home/yingying/opt/fsl_4_1_8/bin/fslcc /home/yingying/opt/fsl_feeds/data/fmri.ica/melodic_IC /home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC > /home/yingying/opt/fsl_feeds/results/fmri.ica/fslcc.txt
** ERROR (nifti_image_read): failed to find header file for '/home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC'
** ERROR: nifti_image_open(/home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC): bad header info
ERROR: failed to open file /home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC
ERROR: Could not open image /home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC
Image Exception : #22 :: Failed to read volume /home/yingying/opt/fsl_feeds/results/fmri.ica/melodic_IC
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted

==============================================
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

=======================
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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