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
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
