Hi,
the problem is here:
--te: Couldn't set_value! valstr="0,022"!
Put this in your .bash_profile
export LC_NUMERIC="en_GB.UTF-8"
Cheers,
Andreas
Am 18.07.13 16:05 schrieb "Marco Castellaro" unter
<[log in to unmask]>:
>Dear All,
>
>I am running FSL 5.0.2.2 on a mac os mountain lion. I am trying to
>co-register a generic EPI (in this case I am co-registering an
>equilibrium magnetization image for ASL calibration) to an anatomical
>3DT1-weighted. I am now using the FEAT/FSL GUI, including only pre-stat.
>I have also already run BET on both EPI and T1. I am also using a
>Fieldmap to account for geometrical distortion in EPI. I have a problem
>running the script with the fieldmap. If I don't include the fieldmap
>step all is working. Since I am not happy with the result I am trying to
>use the fieldmap to improve the registration. Here is the log that I am
>getting:
>
>
>Progress Report / Log
>
>Started at Gio 18 Lug 2013 15:17:56 CEST
>Feat main script
>
>
>/bin/cp /tmp/feat_0oZLD9.fsf design.fsf
>
>/usr/local/fsl/bin/feat_model design
>libc++abi.dylib: terminate called throwing an exception
>
>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 NIFTI/M0B_brain++.feat/design.fsf -D
>NIFTI/M0B_brain++.feat -I 1 -init
>25157
>
>/usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat1b_reg -j 25157
>/usr/local/fsl/bin/feat NIFTI/M0B_brain++.feat/design.fsf -D
>NIFTI/M0B_brain++.feat -I 1 -reg
>25231
>
>/usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat2_pre -j 25231,25157
>/usr/local/fsl/bin/feat NIFTI/M0B_brain++.feat/design.fsf -D
>NIFTI/M0B_brain++.feat -I 1 -prestats
>syntax error in expression "Image + ( 10 * ( Exception - Image ) / 100.0
>)": variable references require preceding $
> 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 25231
>/usr/local/fsl/bin/feat NIFTI/M0B_brain++.feat/design.fsf -D
>NIFTI/M0B_brain++.feat -stop
>
>/usr/local/fsl/bin/mainfeatreg -d NIFTI/M0B_brain++.feat -l
>NIFTI/M0B_brain++.feat/logs/feat5_reg -R
>NIFTI/M0B_brain++.feat/report_unwarp.html -r
>NIFTI/M0B_brain++.feat/report_reg.html -i
>NIFTI/M0B_brain++.feat/example_func.nii.gz -h NIFTI/T1_brain -w BBR -x
>90 -a NIFTI/Fieldmap_phase -b NIFTI/Fieldmap_mag -e 22 -f 10 -g 2.5 -p y-
>-w BBR
>Option -d ( output directory ) selected with argument
>"NIFTI/M0B_brain++.feat"
>Option -l ( logfile )input with argument
>"NIFTI/M0B_brain++.feat/logs/feat5_reg"
>Option -R ( html unwarping report ) selected with argument
>"NIFTI/M0B_brain++.feat/report_unwarp.html"
>Option -r ( html registration report ) selected with argument
>"NIFTI/M0B_brain++.feat/report_reg.html"
>Option -i ( main input ) input with argument
>"NIFTI/M0B_brain++.feat/example_func.nii.gz"
>Option -h ( high-res structural image ) selected with argument
>"NIFTI/T1_brain"
>Option -w ( highres dof ) selected with argument "BBR"
>Option -x ( highres search ) selected with argument "90"
>Option -a ( fieldmap image ) selected with argument
>"NIFTI/Fieldmap_phase"
>Option -b ( field ) selected with argument "NIFTI/Fieldmap_mag"
>Option -e ( echo time ) selected with argument "22"
>Option -f ( signal loss Threshold ) selected with argument "10"
>Option -g ( echo spacing ) selected with argument "2.5"
>Option -p ( phase encoding direction ) selected with argument "y-"
>Option -w ( highres dof ) selected with argument "BBR"
>
>Part of FSL (build 502)
>sigloss
>Copyright(c) 2004, University of Oxford (Mark Jenkinson)
>Estimates signal loss from a field map (in rad/s) - possibly saved by
>fugue
>
>
>Usage:
>sigloss [options] -i b0map -m mask -s sigloss_estimate
>
>Compulsory arguments (You MUST set one or more of):
> -i,--in input b0 map image filename (in rad/s)
> -s,--sigloss output signal loss image filename
>
>Optional arguments (You may optionally specify one or more of):
> -m,--mask input mask filename
> --te echo time (in seconds)
> -d,--slicedir slice direction (either x , y or z)
> -v,--verbose switch on diagnostic messages
> -h,--help display this message
>
>
>
>--te: Couldn't set_value! valstr="0,022"!
>Cannot open volume FM_UD_fmap_sigloss for reading!
>Cannot open volume FM_UD_fmap_sigloss for reading!
>Image Exception : #22 :: ERROR: Could not open image FM_UD_fmap_sigloss
>libc++abi.dylib: terminate called throwing an exception
>Image Exception : #22 :: ERROR: Could not open image FM_UD_sigloss+mag
>libc++abi.dylib: terminate called throwing an exception
>sh: line 1: 25570 Abort trap: 6 /usr/local/fsl/bin/slicer
>FM_UD_sigloss+mag -s 3 -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
>
>
>I think that something wrong is happening with TE value settings..
>
>--te: Couldn't set_value! valstr="0,022"!
>
>I think that something went wrong in the conversion of TE value, in
>particular it should be "0.022" and not "0,022" (22ms).
>
>Is there anyone that can help ma solving this issue?
>
>Thank you
>
>Marco Castellaro
>
>PhD Student
>Department of Information Engineering
>University of Padova
>Via G. Gradenigo 6/B
>35131 - Padova - Italy
>
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