JISCMail - FSL Archives

Hi - it seems that on some OS's there is weird behaviour in the shell - I think the following should fix this. Put the attached file into $FSLDIR/tcl

Does this work?

Cheers.

On 14 Sep 2012, at 11:37, Franklin, Crystal G wrote:

I am running it on Mac OS X 10.7.4.

Crsyatl

From: Stephen Smith <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, September 14, 2012 10:31 AM
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Error

Hi - I can't see what might be causing this - FEAT runs fine on your setup/data on my computer.

Which exact OS are you using? What SGE setup (if any)?

Cheers.

On 14 Sep 2012, at 08:25, Franklin, Crystal G wrote:

Has there been any luck determining what is the cause or solution to this error?

Thanks,

Crystal

From: <Franklin>, ric uthscsa <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, September 11, 2012 9:51 AM
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Error

I am still getting the same error. I have uploaded the data. The reference number is 603990.

Thanks,

Crystal

From: Stephen Smith <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, September 11, 2012 1:47 AM
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Error

Hi - did you read in an old design.fsf into the FEAT GUI and run it from there (or save it and run from the command-line)? In general this should prepare old designs for running with new FEAT.

If that doesn't help, then please upload the data (see upload link on FSL support page on the wiki).

Cheers.

On 10 Sep 2012, at 20:11, Franklin, Crystal G wrote:

Dear FSL,

I installed version 5.0 and I am trying to rerun a previous analysis that worked in the older version. Now when I try running, I get the following error in the log:

/bin/cp /tmp/feat_BEPWaM.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 10 -l logs -N feat0_init   /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -init
10568

/usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat1b_reg -j 10568  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -reg
10648

/usr/local/fsl/bin/fsl_sub -T 12 -l logs -N feat2_pre -j 10648,10568  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -prestats
11213

/usr/local/fsl/bin/fsl_sub -T 78 -l logs -N feat3_film -j 11213  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -I 1 -film
11548

/usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat4_post -j 11548  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -poststats 0 0
child process exited abnormally
    while executing
"if { [ catch {



for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argin..."
    (file "/usr/local/fsl/bin/feat" line 119)

/usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 10648  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -poststats 1 0
child process exited abnormally
    while executing
"if { [ catch {



for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argin..."
    (file "/usr/local/fsl/bin/feat" line 119)

/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 11213,11548,10648  /usr/local/fsl/bin/feat /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/design.fsf -D /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -stop

/usr/local/fsl/bin/mainfeatreg -d /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat -l /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/logs/feat5_reg -R /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_unwarp.html -r /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_reg.html  -i /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/example_func.nii.gz  -h /fmri_data/lovallo3_OFHP/EM0135/EM0135_3d_bet -w  6 -x 90 -s /fmri_data/lovallo3_OFHP/colinbrain/colinbrain_tlrc_2x2x2 -y 12 -z 180 
Option -d ( output directory ) selected with  argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat"
Option -l ( logfile )input with argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/logs/feat5_reg"
Option -R ( html unwarping report ) selected with  argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_unwarp.html"
Option -r ( html registration report ) selected with  argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/report_reg.html"
Option -i ( main input ) input with argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_discount.feat/example_func.nii.gz"
Option -h ( high-res structural image ) selected with  argument "/fmri_data/lovallo3_OFHP/EM0135/EM0135_3d_bet"
Option -w ( highres dof ) selected with  argument "6"
Option -x ( highres search ) selected with  argument "90"
Option -s ( standard image ) selected with  argument "/fmri_data/lovallo3_OFHP/colinbrain/colinbrain_tlrc_2x2x2"
Option -y ( standard dof ) selected with  argument "12"
Option -z ( standard search ) selected with  argument "180"

Initialisation

/usr/local/fsl/bin/fslmaths /fmri_data/lovallo3_OFHP/EM0135/EM0135_discount prefiltered_func_data -odt float
Total original volumes = 120

/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 60 1

Prestats

/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -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

/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

/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet

/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1397.647461 

/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 139.7647461 -Tmin -bin mask -odt char

/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50
1017.465332 

/usr/local/fsl/bin/fslmaths mask -dilF mask

/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh

/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/local/fsl/bin/susan prefiltered_func_data_thresh 763.098999 2.12314225053 3 1 1 mean_func 763.098999 prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 9.82834469686 prefiltered_func_data_intnorm

/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 20.0 -1 prefiltered_func_data_tempfilt

/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*

Stats

mkdir -p custom_timing_files ; /bin/cp /fmri_data/lovallo3_OFHP/designs/discount/discount.txt custom_timing_files/ev1.txt

/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5   filtered_func_data design.mat 1000.0
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=120
paradigm.getDesignMatrix().Ncols()=2
sizeTS=120
numTS=183479
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 9616.25
sig = 1556
Spatially smoothing auto corr estimates
.........
Completed
Tukey M = 10
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results... 
Completed

/usr/local/fsl/bin/smoothest -d 118   -m mask -r stats/res4d > stats/smoothness

Post-stats

/usr/local/fsl/bin/contrast_mgr  stats design.con
child process exited abnormally
    while executing
"if { [ catch {



for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argin..."
    (file "/usr/local/fsl/bin/feat" line 119)
child process exited abnormally
    while executing
"if { [ catch {



for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argin..."
    (file "/usr/local/fsl/bin/feat" line 119)

Any idea what could be causing this?

Thanks,

Crystal

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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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