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Hi, FSL experts

I just figured out the files in /reg could come out when I chose the nonlinear button in registration.  But  filtered_func_data_bp.nii.gz and filtered_func_data_bp_normalized_trilinear.nii.gz could not produced. Do you know where these two files produce?

Mingxia
 
On Wed, Jun 27, 2012 at 12:58 PM, zhang mingxia <[log in to unmask]> wrote:
Hi Dear Experts,

There is some information with which you might know what's the problem. I ran the first level analysis (the prestats) in cluster and there was error I mentioned before: 
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'

Such error would not produce when I ran this analysis in my own computer. I found many files were lost with the error, including 2 files in .feat directory: filtered_func_data_bp.nii.gz/filtered_func_data_bp_normalized_trilinear.nii.gz; 7 files in .feat/reg: highres2standard_jac.nii.gz/highres2standard_linear.nii.gz/highres2standard_warp.nii.gz/highres_head.nii.gz/highres_head_to_standard_head.log/standard_head.nii.gz/standard_mask.nii.gz.
But in error one, in the the .feat/.files, there was a "images" folder which seems a linkto /fsl/4.1.6/doc/images. No this one in the correctly run data.

Mingxia


On Tue, Jun 26, 2012 at 12:21 AM, zhang mingxia <[log in to unmask]> wrote:
Hi Mark,

You come back again! Thank you. I have sent the link to the manager of the cluster. It seems very similar problem. I will try the FEEDS test data and see what will happen.

Mingxia


On Mon, Jun 25, 2012 at 11:58 PM, Mark Jenkinson <[log in to unmask]> wrote:
Dear Mingxia,

I do not know what is happening on your cluster as I have not seen this before.

So I would recommend trying the FEEDS test data to see if that works OK on your cluster (to make sure it isn't something strange in the files you've prepared yourself).

You might also find it useful to look at the following link (that I found using google) as it may be helpful - and although I don't really know anything about it, the contents seemed quite relevant:

All the best,
Mark



On 26 Jun 2012, at 03:35, zhang mingxia wrote:

Hi Christine,

I believe, but not 100% sure that the error should be caused by the FSL program. Because I tried this data in my own computer and there was no error. Another kind guy in my school helped me by using my data in his local computer, also no error. He tried it on the cluster, the same error. 

Now the thing is, besides using the system copy of FSL, I I installed a local FSL in cluster. Error came out in both FSL. Thus, reinstallation of FSL could not resolve the problem. The administrative staff of the cluster in my university is a skilled computer person, but he is not familiar with FSL. If someone could figure out where the error produce, he said he could fix the problem.

He will go to vacation after this Tuesday, I really hope someone knows the resolution. Thanks.

Mingxia 

On Mon, Jun 25, 2012 at 12:16 PM, Christine Zakrzewski <[log in to unmask]> wrote:
Good luck!!
 
Date: Mon, 25 Jun 2012 11:07:57 -0700

From: [log in to unmask]
Subject: Re: [FSL] Some error happened in cluster/server but not in the private computer
To: [log in to unmask]

Hi Christine,

Thank you and FSL group! I cc this email to the administrative staff of the cluster who might have some thought about the problem (He is not in maillist, I don't know whether he could get this email or could send email to you).

About the semicolon, I am not very sure. I created the .fsf file by fsl_gui in linux (direct in the cluster by VNCserver, I did not move it to window) so I thought there should not be such problem in the .fsf script. 

Thanks again.

Mingxia

On Mon, Jun 25, 2012 at 1:41 AM, Christine Zakrzewski <[log in to unmask]> wrote:
I am not actually sure where your errors are occuring, and am now entirely confused.
Now that Steven has joined the conversation, he can maybe shed some light on the problem--arent the semicolon characters throughtout the feat script a problem, as the semicolon is a special character indicating to continue to next line?
Christine 
 
Date: Mon, 25 Jun 2012 01:09:10 -0700
From: [log in to unmask]
Subject: Re: [FSL] Some error happened in cluster/server but not in the private computer
To: [log in to unmask]

Sorry. I attached two times of the right one. Now it is the error one in attachment. I also attached the logs folder.

Yes, I tried on my private computer, no problem.  I checked design.fsf for many times. It should be the problem on the cluster setup.

The administrative staff said if I can find out where the error happen (like which script of fsl program was being executed when error came out ), he could figure out it. 



On Mon, Jun 25, 2012 at 12:09 AM, Stephen Smith <[log in to unmask]> wrote:
Hi - did you confirm that your .fsf file runs correctly just on a local computer - e.g.

feat design.fsf

That should help you work out if the problem is in your design.fsf or on the cluster setup.

The error message you are getting is not a familiar one.  If your admin looks at the individual error and log files in the "logs" directory inside the FEAT output directory.

Cheers.





On 25 Jun 2012, at 02:53, zhang mingxia wrote:

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

<report_log.html>


---------------------------------------------------------------------------
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
---------------------------------------------------------------------------






--Forwarded Message Attachment--

Progress Report / Log

Started at Wed Jun 13 12:16:49 PDT 2012 Feat main script
/bin/cp /tmp/feat_yNnJoc.fsf design.fsf

/apps/fsl/4.1.6/bin/feat_model design 


mkdir .files;cp /apps/fsl/4.1.6/doc/fsl.css .files;ln -s /apps/fsl/4.1.6/doc/images .files/images

/apps/fsl/4.1.6/bin/fsl_sub -T 24 -l logs -N feat2_pre -j featModelID  /apps/fsl/4.1.6/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
2112438

/apps/fsl/4.1.6/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 2112438  /apps/fsl/4.1.6/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
2112439

/apps/fsl/4.1.6/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 2112438,2112439  /apps/fsl/4.1.6/bin/feat /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat/design.fsf -D /home/mingxiaz/data/Restingstate_Training/try/try_pre+.feat -stop
2112440
Prestats
/apps/fsl/4.1.6/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!

/apps/fsl/4.1.6/bin/fslroi prefiltered_func_data prefiltered_func_data 5 235

/apps/fsl/4.1.6/bin/fslroi prefiltered_func_data example_func 117 1

/apps/fsl/4.1.6/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 117 -rmsrel -rmsabs

/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

/apps/fsl/4.1.6/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 

/apps/fsl/4.1.6/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 

/apps/fsl/4.1.6/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 

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func

/apps/fsl/4.1.6/bin/bet2 mean_func mask -f 0.3 -n -m; /apps/fsl/4.1.6/bin/immv mask_mask mask

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/apps/fsl/4.1.6/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 974.761292 

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_bet -thr 97.4761292 -Tmin -bin mask -odt char

/apps/fsl/4.1.6/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
820.489075 

/apps/fsl/4.1.6/bin/fslmaths mask -dilF mask

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/apps/fsl/4.1.6/bin/susan prefiltered_func_data_thresh 615.36680625 2.12314225053 3 1 1 mean_func 615.36680625 prefiltered_func_data_smooth

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_smooth -inm 10000 prefiltered_func_data_intnorm

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_intnorm -bptf 37.5 -1 prefiltered_func_data_tempfilt

/apps/fsl/4.1.6/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/apps/fsl/4.1.6/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

/apps/fsl/4.1.6/bin/fslmaths /home/mingxiaz/data/Restingstate_Training/try/3d_brain highres

/apps/fsl/4.1.6/bin/fslmaths /home/mingxiaz/apps/fsl/data/standard/MNI152_T1_2mm_brain standard

/apps/fsl/4.1.6/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  

/apps/fsl/4.1.6/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat

/apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png

/apps/fsl/4.1.6/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  

/apps/fsl/4.1.6/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat

/apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png

/apps/fsl/4.1.6/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat

/apps/fsl/4.1.6/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear

/apps/fsl/4.1.6/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat

/apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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 ; /apps/fsl/4.1.6/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'