Hi,
I agree that the comma/locale issue a problem and needs fixing.
I'm also concerned about:
libc++abi.dylib: terminate called throwing an exception
which is something I haven't seen before.
Did you do a standard installation?
Maybe someone else can help shed some light on this error too.
All the best,
Mark
On 18 Jul 2013, at 16:26, Andreas Bartsch <[log in to unmask]> wrote:
> 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
>>
>> [log in to unmask]
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