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Hi - the log you sent previously did have error messages in it - so please can you confirm that you are indeed seeing these errors on the logs even when you run FEAT on your local computer?   This suggests that there is a mistake in your design.fsf file,.

Cheers.


On 25 Jun 2012, at 08:27, zhang mingxia wrote:

Hi Christine,

Thank you for your kind suggestion. I had modified .bashrc file before running .fsf file by the command from FSL website:
FSLDIR=/home/mingxiaz/apps/fsl
PATH=${FSLDIR}/bin:${PATH} 
export FSLDIR PATH

I attached the wrong log in last letter. That log came out when I ran .fsf by my local FSL program in server. I really want to resolved the problem which came out when I ran .fsf by the system copy of FSL program (actually, the same errors). See the attachment. The administrative staff of server installed this program. We thought some scripts in FSL program are bad in the server environment, but we did not know which ones. Can you figure out by the log?

One phenomenon is that the error came out very quickly after I ran the .fsf script.  It came out right after or before when this command was executed: /apps/fsl/4.1.6/bin/fslmaths /home/mingxiaz/data/Restingstate_Training/try2/Audiovisual1 prefiltered_func_data -odt float. And then, other command, such as the fslroi and mcflirt will continue to be executed. 

For comparison, I put two logs in attachment, the log.error is the abnormally running one and log.right is the correct one with the same data in different server.  

I saw the first different place was:
home/mingxiaz/apps/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 117 -rmsrel -rmsabs
refnum = 117
Original_refvol = 117 (the correct one)
The error one, there is no "refnum = 117 Original_refvol = 117" 

The big difference is the absence of the execution of command below in error one:
/opt/fmritools/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 /opt/fmritools/fsl/bin/fnirt --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2standard_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=10,10,10 Setting subsampling Setting reg mode Setting lambda Setting subsampling Setting reg mode Setting lambda SpMat::SolveForx: Warning requested tolerence not obtained. Requested tolerance was 0.001, and achieved tolerance was 0.0629956 This may or may not be a problem in your application, but you should look into it Setting subsampling Setting reg mode Setting lambda Setting subsampling Setting reg mode Setting lambda Setting subsampling Setting reg mode Setting lambda /opt/fmritools/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png /opt/fmritools/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat /opt/fmritools/fsl/bin/applywarp --ref=standard --in=example_func --out=example_func2standard --warp=highres2standard_warp --premat=example_func2highres.mat /opt/fmritools/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/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 ; /opt/fmritools/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png
BTW, there is an absence of filtered_func_data_bp.nii.gz, filtered_func_data_bp_normalized_trilinear.nii.gz and many files in .feat/reg.

Does this information make sense? I am not familiar with the scripts in fsl/bin. Hope you can give me some suggestion by the information I provide. Thanks.

Mingxia







 



On Sun, Jun 24, 2012 at 8:22 PM, Christine Zakrzewski <[log in to unmask]> wrote:
maybe the $FSLDIR variable is not set on the network?
if the networked fsl program is located at: /home/mingxiaz/apps/fsl/bin
before you run the script, type in the shell:
FSLDIR=/home/mingxiaz/apps/fsl/bin
export $FSLDIR
then just to check everything went right, type in the shell:
echo $FSLDIR
the commands may be slighly different if you are not in the bash shell.
this will only work in the current session, if you require a more permanent solution--modify .bash.rc file with the same commands.
good luck--christine
 
Date: Sun, 24 Jun 2012 18:53:07 -0700
From: [log in to unmask]
Subject: [FSL] Some error happened in cluster/server but not in the private computer
To: [log in to unmask]


Dear FSL experts,

Sorry to bring this problem again. Very hopefully that some one knows the problem below:

I was running the first-level analysis of some functional data recent in a cluster/server and got this error:: /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module'. People would always think there are problems with the .fsf script. But I created the .fsf script by FSL in Linux environment and did not move it to Windows. The interesting thing is that I could run the data normally in my own computer without any error by the same version of FSL with the same way. 

The administrative staff of the the server is very nice to want to figure out the problem. He thought there was something wrong with some FSL program scripts in cluster/server environment. But we could not know which script the .fsf script (the .fsf script is very brief, it will ask many scripts in FSL program) called when the error came out. 

Any one who met such problem before just on cluster/server? 

Attachment is the report log. Does any body know what script of FSL program was executed when the error came out? 

I really appreciate to get the reply. Thanks.

Mingxia



--Forwarded Message Attachment--

Progress Report / Log

Started at Sat Jun 23 23:43:56 PDT 2012 Feat main script
/bin/cp /home/mingxiaz/data/Restingstate_Training/try/try_pre.fsf design.fsf

/home/mingxiaz/apps/fsl/bin/feat_model design 

mkdir .files;cp /home/mingxiaz/apps/fsl/doc/fsl.css .files;ln -s /home/mingxiaz/apps/fsl/doc/images .files/images

/home/mingxiaz/apps/fsl/bin/fsl_sub -T 24 -l logs -N feat2_pre -j featModelID  /home/mingxiaz/apps/fsl/bin/feat /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat/design.fsf -D /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat -I 1 -prestats
2114894

/home/mingxiaz/apps/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 2114894  /home/mingxiaz/apps/fsl/bin/feat /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat/design.fsf -D /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat -I 1 -reg
2114895

/home/mingxiaz/apps/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 2114894,2114895  /home/mingxiaz/apps/fsl/bin/feat /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat/design.fsf -D /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat -stop
2114896
Prestats
/home/mingxiaz/apps/fsl/bin/fslmaths /home/mingxiaz/data/Restingstate_Training/try/rest prefiltered_func_data -odt float
Total original volumes = 240
Deleting 5 volume(s) - BE WARNED for future analysis!

/home/mingxiaz/apps/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 5 235

/home/mingxiaz/apps/fsl/bin/fslroi prefiltered_func_data example_func 117 1

/home/mingxiaz/apps/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 117 -rmsrel -rmsabs
refnum = 117
Original_refvol = 117

/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

/home/mingxiaz/apps/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 

/home/mingxiaz/apps/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 

/home/mingxiaz/apps/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 

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/home/mingxiaz/apps/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /home/mingxiaz/apps/fsl/bin/immv mask_mask mask

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/home/mingxiaz/apps/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 974.761292 

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_bet -thr 97.4761292 -Tmin -bin mask -odt char

/home/mingxiaz/apps/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
820.489075 

/home/mingxiaz/apps/fsl/bin/fslmaths mask -dilF mask

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/home/mingxiaz/apps/fsl/bin/susan prefiltered_func_data_thresh 615.36680625 2.12314225053 3 1 1 mean_func 615.36680625 prefiltered_func_data_smooth

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_smooth -inm 10000 prefiltered_func_data_intnorm

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 37.5 -1 prefiltered_func_data_tempfilt

/home/mingxiaz/apps/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/home/mingxiaz/apps/fsl/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'
Registration
/bin/mkdir -p reg

/home/mingxiaz/apps/fsl/bin/fslmaths /home/mingxiaz/data/Restingstate_Training/try/3d_brain highres

/home/mingxiaz/apps/fsl/bin/fslmaths /home/mingxiaz/apps/fsl/data/standard/MNI152_T1_2mm_brain standard

/home/mingxiaz/apps/fsl/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  

/home/mingxiaz/apps/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat

/home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png

/home/mingxiaz/apps/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  

/home/mingxiaz/apps/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat

/home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png

/home/mingxiaz/apps/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat

/home/mingxiaz/apps/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear

/home/mingxiaz/apps/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat

/home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/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 ; /home/mingxiaz/apps/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'


























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