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FSL  August 2009

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Subject:

Re: Error-Feat 1st level

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 17 Aug 2009 12:05:58 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (631 lines)

HI - no, see the very top of your logfile - your original input data  
isn't valid - it looks like your file has been corrupted as it doesn't  
contain enough data according to the header.
Cheers.

On 14 Aug 2009, at 22:45, Mona Lisa Chanda wrote:

> Hi,
>
> I've tried to run the same FEAT analysis 3 times and keep getting  
> error
> messages. There doesn't appear to be anything wrong with the input  
> files or
> the preprocessing (filtered functional data looks good). But, the  
> stats still
> aren't running properly. I've attached the log file, if anybody  
> knows what the
> problem is or how to fix it, please let me know.
>
> Thanks!
> Mona
>
> Progress Report / Log
> Started at Wed Feb 1 18:54:27 CST 2006
> Feat main script
>
>
>
> /bin/cp /tmp/feat_KHTnrg.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 24 -l logs -N feat2_pre   /usr/local/ 
> fsl/bin/feat /home/mona/Endo/pat009/Scan1/sp1_7pt_lowpass_full.feat/ 
> design.fsf -D /home/mona/Endo/pat009/Scan1/sp1_7pt_lowpass_full.feat  
> -I 1 -prestats
> 23579
>
> /usr/local/fsl/bin/fsl_sub -T 24 -l logs -N feat3_film -j 23579  / 
> usr/local/fsl/bin/feat /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat/design.fsf -D /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat -I 1 -film
> 23580
>
> /usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat4_post -j 23580  /usr/ 
> local/fsl/bin/feat /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat/design.fsf -D /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat -poststats 0 0
> 23581
>
> /usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 23579  /usr/ 
> local/fsl/bin/feat /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat/design.fsf -D /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat -I 1 -reg
> 23582
>
> /usr/local/fsl/bin/fsl_sub -T 15 -l logs -N feat4_post -j  
> 23581,23582  /usr/local/fsl/bin/feat /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat/design.fsf -D /home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.feat -poststats 1 0
> 23583
>
> /usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j  
> 23579,23580,23583,23582  /usr/local/fsl/bin/feat /home/mona/Endo/ 
> pat009/Scan1/sp1_7pt_lowpass_full.feat/design.fsf -D /home/mona/Endo/ 
> pat009/Scan1/sp1_7pt_lowpass_full.feat -stop
> 23584
>
>
> --------------------------------------------------------------------------------
> Prestats
>
>
> /usr/local/fsl/bin/fslmaths /home/mona/Endo/pat009/Scan1/sp1  
> prefiltered_func_data -odt float
> Total original volumes = 244
> Deleting 4 volume(s) - BE WARNED for future analysis!
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data  
> prefiltered_func_data 4 240
> ++ WARNING: nifti_read_buffer(prefiltered_func_data.nii.gz):
>   data bytes needed = 589824
>   data bytes input  = 159706
>   number missing    = 430118 (set to 0)
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 120 1
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out  
> prefiltered_func_data_mcf -mats -plots -refvol 120 -rmsrel -rmsabs
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
>
> /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
> can't read "absrms": no such variable
>    while executing
> "expr int($absrms*100.0)/100.0 "
>    (procedure "feat5:proc_prestats" line 101)
>    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 "/usr/local/fsl/bin/feat" line 137)
>
>
> --------------------------------------------------------------------------------
> Stats
>
>
> mkdir -p custom_timing_files ; /bin/cp /home/mona/Endo/pat009/txt/ 
> scan1/avg_sp1_7.txt custom_timing_files/ev1.txt
>
> cp mc/prefiltered_func_data_mcf.par confoundevs.txt
>
> /usr/local/fsl/bin/feat_model design confoundevs.txt
> terminate called after throwing an instance of  
> 'NEWMAT::IncompatibleDimensionsException'
> 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 "/usr/local/fsl/bin/feat" line 137)
>
>
> --------------------------------------------------------------------------------
> Post-stats
>
>
> /usr/local/fsl/bin/contrast_mgr  stats design.con
>
>
> An exception has been thrown
> design.con is not a valid vest fileTrace: ContrastMgr::Load;  
> ContrastMgr::run.
>
> couldn't change working directory to "/home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.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 "/usr/local/fsl/bin/feat" line 137)
> couldn't change working directory to "/home/mona/Endo/pat009/Scan1/ 
> sp1_7pt_lowpass_full.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 "/usr/local/fsl/bin/feat" line 137)
>
>
> --------------------------------------------------------------------------------
> Registration
>
>
> /bin/mkdir -p reg
>
> /usr/local/fsl/bin/fslmaths /home/mona/Endo/pat009/Scan1/t1_brain  
> highres
>
> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/ 
> MNI152_T1_2mm_brain standard
>
> /usr/local/fsl/bin/flirt -ref highres -in example_func -out  
> example_func2highres -omat example_func2highres.mat -cost corratio - 
> dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp  
> trilinear
>
> /usr/local/fsl/bin/convert_xfm -inverse -omat  
> highres2example_func.mat example_func2highres.mat
> Cannot read input-matrix
>
> /usr/local/fsl/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 ; /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_func2highres1.png ; /usr/local/fsl/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 ; /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_func2highres2.png ; / 
> usr/local/fsl/bin/pngappend example_func2highres1.png -  
> example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png
> WARNING: input image is empty
>
> /usr/local/fsl/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
>
> /usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat  
> highres2standard.mat
>
> /usr/local/fsl/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 ; /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  
> highres2standard1.png ; /usr/local/fsl/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 ; /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 highres2standard2.png ; /usr/ 
> local/fsl/bin/pngappend highres2standard1.png -  
> highres2standard2.png highres2standard.png; /bin/rm -f sl?.png
>
> /usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat - 
> concat highres2standard.mat example_func2highres.mat
> Cannot read input-matrix
>
> /usr/local/fsl/bin/flirt -ref standard -in example_func -out  
> example_func2standard -applyxfm -init example_func2standard.mat - 
> interp trilinear
> Could not open matrix file example_func2standard.mat
>
> /usr/local/fsl/bin/convert_xfm -inverse -omat  
> standard2example_func.mat example_func2standard.mat
> Could not open matrix file example_func2standard.mat
> Cannot read input-matrix
>
> /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
> ** 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'
> sh: line 1: 11062 Aborted                 (core dumped) /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
>
> Cannot open sla.png for reading
> sh: line 1: 11064 Segmentation fault      (core dumped) /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
> ** 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'
> sh: line 1: 11065 Aborted                 (core dumped) /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
>
> Cannot open sla.png for reading
> sh: line 1: 11066 Segmentation fault      (core dumped) /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
>
> Cannot open example_func2standard1.png for reading
> sh: line 1: 11067 Segmentation fault      (core dumped) /usr/local/ 
> fsl/bin/pngappend example_func2standard1.png -  
> example_func2standard2.png example_func2standard.png
>
>
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---------------------------------------------------------------------------
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
---------------------------------------------------------------------------

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