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Subject:

Re: FEAT - Error

From:

paul mccarthy <[log in to unmask]>

Reply-To:

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

Date:

Thu, 15 Nov 2018 11:01:20 +0000

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (502 lines) 

Hi Hashi,

This error implies that your FSL installation is not complete - follow
the steps at this link to fix your installation:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation

Cheers,

Paul

On 14/11/2018, Hashi <[log in to unmask]> wrote:
> Hello fsl experts,
>
> I'm attempting to run registration for some of my data using FEAT.
> Unfortunately, when ever I run FEAT from the gui I receive the following
> output message:
>
> Progress Report / Log
> Started at Tue Nov 13 11:16:57 EST 2018
> Feat main script
>
>
> /bin/cp /tmp/feat_nEWb1t.fsf design.fsf
>
> mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r
> /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
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/design.fsf -D
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat -I 1 -init
> 20509
>
> /usr/local/fsl/bin/fsl_sub -T 267 -l logs -N feat2_pre -j 20509
> /usr/local/fsl/bin/feat
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/design.fsf -D
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat -I 1 -prestats
> child process exited abnormally
>     while executing
> "if { [ catch {
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr arginde..."
>     (file "/usr/local/fsl/bin/feat" line 312)
>
> FATAL ERROR ENCOUNTERED:
> COMMAND:
> /usr/local/fsl/bin/fsl_sub -T 267 -l logs -N feat2_pre -j 20509
> /usr/local/fsl/bin/feat
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/design.fsf -D
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat -I 1 -prestats
> ERROR MESSAGE:
> child process exited abnormally
> END OF ERROR MESSAGE
> Initialisation
>
> /usr/local/fsl/bin/fslmaths
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/sub-1B_task-comparison_bold_4d
> prefiltered_func_data -odt float
> Total original volumes = 600
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 300 1
> Preprocessing:Stage 1
>
> /usr/local/fsl/bin/mainfeatreg -F 6.00 -d
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat -l
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/logs/feat2_pre -R
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_unwarp.html -r
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_reg.html  -i
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/example_func.nii.gz
> -h /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain -w  BBR
> -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
> Option -F ( FEAT version parameter ) selected with  argument "6.00"
> Option -d ( output directory ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat"
> Option -l ( logfile )input with argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/logs/feat2_pre"
> Option -R ( html unwarping report ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_reg.html"
> Option -i ( main input ) input with argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/example_func.nii.gz"
> Option -h ( high-res structural image ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain"
> Option -w ( highres dof ) selected with  argument "BBR"
> Option -x ( highres search ) selected with  argument "90"
> 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"
> Registration
>
> /bin/mkdir -p /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/reg
>
> /usr/local/fsl/bin/mainfeatreg: line 504: /usr/local/fsl/bin/imcp: No such
> file or directory
>
> /usr/local/fsl/bin/fslmaths
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain highres
>
>
> /usr/local/fsl/bin/fslmaths
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w  highres_head
>
>
> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain
> standard
>
> did not find file: example_func2highres.mat. Generating transform.
>
> /usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head
> --t1brain=highres --out=example_func2highres
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 331: 21397 Aborted                 (core
> dumped) $FSLDIR/bin/flirt -ref ${vrefbrain} -in ${vepi} -dof 6 -omat
> ${vout}_init.mat
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 392: 21399 Aborted                 (core
> dumped) $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr
> -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out
> ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
> Could not open matrix file example_func2highres.mat
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 392: 21401 Aborted                 (core
> dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
> --premat=${vout}.mat --interp=spline
> Running FAST segmentation FLIRT pre-alignment Running BBR
>
> /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
> example_func2highres2.png
> Image Exception : #22 :: ERROR: Could not open image example_func2highres
>
>  Cannot open sla.png for reading
> Segmentation fault (core dumped)
>
>  Cannot open example_func2highres1.png for reading
> Segmentation fault (core dumped)
> Error in slicer input, exiting...
>
> /bin/rm example_func2highres1.png
> /bin/rm: cannot remove 'example_func2highres1.png': No such file or
> directory
>
> did not find file: highres2standard.mat. Generating transform.
>
> /usr/local/fsl/bin/flirt -in highres -ref standard -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 highres2standard2.png
>
>
> /bin/rm highres2standard1.png
>
>
> /usr/local/fsl/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
>
> 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
> -searchrx -  -searchry -  -searchrz -  -interp trilinear
> Unrecognised option -
>
>
> /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
> Image Exception : #22 :: ERROR: Could not open image example_func2standard
>
>  Cannot open sla.png for reading
> Segmentation fault (core dumped)
>
>  Cannot open example_func2standard1.png for reading
> Segmentation fault (core dumped)
> Error in slicer input, exiting...
> Preprocessing:Stage 2
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs
> -spline_final
>
> /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/fslmaths prefiltered_func_data_mcf -Tmean mean_func
>
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
> mask_mask mask
> sh: 1: /usr/local/fsl/bin/immv: not found
>
> FATAL ERROR ENCOUNTERED:
> COMMAND:
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
> mask_mask mask
> ERROR MESSAGE:
> child process exited abnormally
> END OF ERROR MESSAGE
> Preprocessing:Stage 1
>
> /usr/local/fsl/bin/mainfeatreg -F 6.00 -d
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat -l
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/logs/feat2_pre -R
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_unwarp.html -r
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_reg.html  -i
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/example_func.nii.gz
> -h /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain -w  BBR
> -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
> Option -F ( FEAT version parameter ) selected with  argument "6.00"
> Option -d ( output directory ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat"
> Option -l ( logfile )input with argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/logs/feat2_pre"
> Option -R ( html unwarping report ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/report_reg.html"
> Option -i ( main input ) input with argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/example_func.nii.gz"
> Option -h ( high-res structural image ) selected with  argument
> "/media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain"
> Option -w ( highres dof ) selected with  argument "BBR"
> Option -x ( highres search ) selected with  argument "90"
> 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"
> Registration
>
> /bin/mkdir -p /media/brain3dviz/IkhlasHashi/Data_/sub-1B/func/+.feat/reg
>
> /usr/local/fsl/bin/mainfeatreg: line 504: /usr/local/fsl/bin/imcp: No such
> file or directory
>
> /usr/local/fsl/bin/fslmaths
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w_brain highres
>
>
> /usr/local/fsl/bin/fslmaths
> /media/brain3dviz/IkhlasHashi/Data_/sub-1B/anat/sub-1B_T1w  highres_head
>
>
> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain
> standard
>
> did not find file: example_func2highres.mat. Generating transform.
>
> /usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head
> --t1brain=highres --out=example_func2highres
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 331: 23797 Aborted                 (core
> dumped) $FSLDIR/bin/flirt -ref ${vrefbrain} -in ${vepi} -dof 6 -omat
> ${vout}_init.mat
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 392: 23799 Aborted                 (core
> dumped) $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr
> -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out
> ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
> Could not open matrix file example_func2highres.mat
> Image Exception : #22 :: ERROR: Could not open image example_func
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/epi_reg: line 392: 23801 Aborted                 (core
> dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
> --premat=${vout}.mat --interp=spline
> Running FAST segmentation FLIRT pre-alignment Running BBR
>
> /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
> example_func2highres2.png
> Image Exception : #22 :: ERROR: Could not open image example_func2highres
>
>  Cannot open sla.png for reading
> Segmentation fault (core dumped)
>
>  Cannot open example_func2highres1.png for reading
> Segmentation fault (core dumped)
> Error in slicer input, exiting...
>
> /bin/rm example_func2highres1.png
> /bin/rm: cannot remove 'example_func2highres1.png': No such file or
> directory
>
> did not find file: highres2standard.mat. Generating transform.
>
> /usr/local/fsl/bin/flirt -in highres -ref standard -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 highres2standard2.png
>
>
> /bin/rm highres2standard1.png
>
>
> /usr/local/fsl/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
>
> 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
> -searchrx -  -searchry -  -searchrz -  -interp trilinear
> Unrecognised option -
>
>
> /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
> Image Exception : #22 :: ERROR: Could not open image example_func2standard
>
>  Cannot open sla.png for reading
> Segmentation fault (core dumped)
>
>  Cannot open example_func2standard1.png for reading
> Segmentation fault (core dumped)
> Error in slicer input, exiting...
> Preprocessing:Stage 2
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs
> -spline_final
>
> /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/fslmaths prefiltered_func_data_mcf -Tmean mean_func
>
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
> mask_mask mask
> sh: 1: /usr/local/fsl/bin/immv: not found
>
> FATAL ERROR ENCOUNTERED:
> COMMAND:
> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
> mask_mask mask
> ERROR MESSAGE:
> child process exited abnormally
> END OF ERROR MESSAGE
> child process exited abnormally
>     while executing
> "if { [ catch {
>
> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>     switch -- [ lindex $argv $argindex ] {
>
> 	-I {
> 	    incr arginde..."
>     (file "/usr/local/fsl/bin/feat" line 312)
> Error encountered while running in main feat script, halting.
> child process exited abnormally
>
> I loaded my 4d functional, as well as my structural.
>
> Any suggestions on what steps I should take next would be much appreciated!
>
>
>
> Thank you so much for your time.
> Sincerely,
> Hashi
>
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