Hi Matthew and MArk,
I am just confirming that this also fixes the error on OSX.
Have a nice weekend!
Cheers,
Andreas
Von: Matthew Webster <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Freitag, 11. Januar 2013 17:55
An: <[log in to unmask]>
Betreff: Re: [FSL] BBR error due to wrong locale settings (SOLVED)
Dear Pavel and Andreas ,
We now make greater usage
of floating-point calculations in our scripts, which unfortunately causes
problems with some non-english shell localisation settings. For now we
suggest setting the numeric-localisation setting to english in your shell
profile when using FSL tools:
export LC_NUMERIC="en_GB.UTF-8"
and we will be forcing this locale setting in fsl.sh from the next patch
onwards.
I hope this helps
Kind Regards
Matthew
> Dear Mark,
>
> I am sorry it took me so long to answer. I tried Bet and everything went fine.
> However, the problem with BBR is not (in my opinion) caused by float point
> number, since the input EPI TE in the Feat GUI is integer and the value is
> obviously converted to float internally when the feat script starts (i.e. when
> I set 41 in the log appears 0,041). I tried the BBR again today (with all
> updates from NeuroDebian), and I got the same error as before. It works,
> however, when started after the LANG variable is changed to en_GB.
>
> Kind regards
>
> Pavel
>
> On 23 November 2012 16:30, Mark Jenkinson <[log in to unmask]> wrote:
>> No - sorry - I haven't been able to replicate this here.
>> I have heard about another instance on a German computer though.
>> Do you ever see this behaviour in other GUIs?
>> For example, if you try the BET GUI and change the fractional intensity
>> threshold to some other value (e.g. 0.3), does this also cause a similar
>> problem?
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 23 Nov 2012, at 14:02, Pavel Hok <[log in to unmask]> wrote:
>>
>>> Dear Mark,
>>>
>>> did you have any luck reproducing the error? I am still getting the same
>>> error with BBR, when I forget to change the locale (I had to add the export
>>> command to my scripts to avoid the issue).
>>>
>>> Kind regards
>>>
>>> Pavel
>>>
>>> On 19 October 2012 16:51, Pavel Hok <[log in to unmask]> wrote:
>>>> Dear Mark,
>>>>
>>>> it is cs_CZ.UTF-8
>>>>
>>>> Thanks for looking into that issue!
>>>>
>>>> Pavel
>>>>
>>>>
>>>> On 19 October 2012 09:26, Mark Jenkinson <[log in to unmask]> wrote:
>>>>> Hi,
>>>>>
>>>>> This is very odd because we simply use calls that we've used for years
>>>>> without problems before.
>>>>> What is your LANG variable usually set to?
>>>>> I'd like to try and replicate the behaviour here.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 19 Oct 2012, at 08:24, Pavel Hok <[log in to unmask]> wrote:
>>>>>
>>>>>> I would like to note as well, that otherwise Feat copes well with the
>>>>>> Czech locale settings. It is really an isolated issue of sigloss or the
>>>>>> routine which processes the input from GUI.
>>>>>>
>>>>>> Kind regards
>>>>>>
>>>>>> Pavel
>>>>>>
>>>>>> On 19 October 2012 09:13, Pavel Hok <[log in to unmask]> wrote:
>>>>>>> Dear Mark,
>>>>>>>
>>>>>>> this issue was, however, not due to wrong input, but rather an internal
>>>>>>> one. The TE is set in ms in the gui, so user cannot affect that
>>>>>>> behaviour unfortunately. The value with comma is converted internally.
>>>>>>> Only switching to English locale helps.
>>>>>>>
>>>>>>> Kind regards
>>>>>>>
>>>>>>> Pavel
>>>>>>>
>>>>>>> On 12 October 2012 18:59, Mark Jenkinson <[log in to unmask]> wrote:
>>>>>>> Dear Pavel,
>>>>>>>
>>>>>>> This behaviour is not restricted sigloss, BBR or Feat.
>>>>>>> Every FSL program requires decimal points rather than commas to be used.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Mark
>>>>>>>
>>>>>>>
>>>>>>> On 12 Oct 2012, at 17:33, Pavel Hok <[log in to unmask]> wrote:
>>>>>>>
>>>>>>> Dear FSL experts,
>>>>>>>
>>>>>>> I have encountered an error after running a single subject analysis in
>>>>>>> Feat using BBR registration and B0 unwarping. I noticed this line in the
>>>>>>> main Feat script log: --te: Couldn't set_value! valstr="0,041"! It
>>>>>>> seems, that the program sigloss cannot cope with the Czech locale,
>>>>>>> where coma is used instead of decimal point. After setting export
>>>>>>> LANG="en_GB" before running feat in the same shell. Afterwards
>>>>>>> everything ran fine.
>>>>>>>
>>>>>>> Feat main script
>>>>>>>
>>>>>>> /bin/cp /tmp/feat_z1wN0E.fsf design.fsf
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/feat_model design
>>>>>>>
>>>>>>> mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;ln -s
>>>>>>> /usr/share/fsl/5.0/doc/images .files/images
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init
>>>>>>> /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -I 1 -init
>>>>>>> 21239
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 60 -l logs -N feat1b_reg -j 21239
>>>>>>> /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -I 1 -reg
>>>>>>> 21321
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 48 -l logs -N feat2_pre -j 21321,21239
>>>>>>> /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -I 1 -prestats
>>>>>>> 24156
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 5 -l logs -N feat3_film -j 24156
>>>>>>> /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -I 1 -film
>>>>>>> 25595
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 0 -l logs -N feat4_post -j 25595
>>>>>>> /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -poststats 0 0
>>>>>>> 25764
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j
>>>>>>> 25764,21321 /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -poststats 1 0
>>>>>>> 26422
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/fsl_sub -T 1 -l logs -N feat5_stop -j
>>>>>>> 24156,25595,26422,21321 /usr/share/fsl/5.0/bin/feat
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/design.fsf -D
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -stop
>>>>>>>
>>>>>>> /usr/share/fsl/5.0/bin/mainfeatreg -d
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat -l
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/logs/feat5_reg -R
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/report_unwarp.html
>>>>>>> -r /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/report_reg.html
>>>>>>> -i
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/example_func.nii.g
>>>>>>> z -n 10 -h /md4/TM-PMP/TM-PMP-888/Results/Mprage_brain -w BBR -x 90 -s
>>>>>>> /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -a
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/Fieldmap_rad -b
>>>>>>> /md4/TM-PMP/TM-PMP-888/Results/Fieldmap_brain -e 41 -f 10 -g 0.69 -p y-
>>>>>>> -w BBR
>>>>>>> Option -d ( output directory ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat"
>>>>>>> Option -l ( logfile )input with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/logs/feat5_reg"
>>>>>>> Option -R ( html unwarping report ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/report_unwarp.htm
>>>>>>> l"
>>>>>>> Option -r ( html registration report ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/report_reg.html"
>>>>>>> Option -i ( main input ) input with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/RHand1_1_fieldmap.feat/example_func.nii.
>>>>>>> gz"
>>>>>>> Option -n ( use nonlinear reg ) input with argument "10"
>>>>>>> Option -h ( high-res structural image ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/Mprage_brain"
>>>>>>> Option -w ( highres dof ) selected with argument "BBR"
>>>>>>> Option -x ( highres search ) selected with argument "90"
>>>>>>> Option -s ( standard image ) selected with argument
>>>>>>> "/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain"
>>>>>>> Option -y ( standard dof ) selected with argument "12"
>>>>>>> Option -z ( standard search ) selected with argument "90"
>>>>>>> Option -a ( fieldmap image ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/Fieldmap_rad"
>>>>>>> Option -b ( field ) selected with argument
>>>>>>> "/md4/TM-PMP/TM-PMP-888/Results/Fieldmap_brain"
>>>>>>> Option -e ( echo time ) selected with argument "41"
>>>>>>> Option -f ( signal loss Threshold ) selected with argument "10"
>>>>>>> Option -g ( echo spacing ) selected with argument "0.69"
>>>>>>> Option -p ( phase encoding direction ) selected with argument "y-"
>>>>>>> Option -w ( highres dof ) selected with argument "BBR"
>>>>>>>
>>>>>>> Part of FSL (build 501)
>>>>>>> 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="0,041"!
>>>>>>> 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
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>> Image Exception : #22 :: ERROR: Could not open image FM_UD_sigloss+mag
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>>
>>>>>>> Cannot open sla.png for reading
>>>>>>> Segmentation fault
>>>>>>> rm: nelze odstranit „sl?.png“: Adresář nebo soubor neexistuje
>>>>>>> intial HighresImage
>>>>>>>
>>>>>>> (standard_in) 1: syntax error
>>>>>>> (standard_in) 1: Error: comparison in expression
>>>>>>> (standard_in) 1: syntax error
>>>>>>> (standard_in) 1: syntax error
>>>>>>> (standard_in) 1: Error: comparison in expression
>>>>>>> (standard_in) 1: syntax error
>>>>>>> /usr/share/fsl/5.0/bin/epi_reg: 172: [: =: unexpected operator
>>>>>>>
>>>>>>> Part of FSL (build 501)
>>>>>>> fugue
>>>>>>> FMRIB's Utility for Geometric Unwarping of EPIs
>>>>>>> Copyright(c) 2000-2008, University of Oxford (Mark Jenkinson)
>>>>>>>
>>>>>>> Usage:
>>>>>>> fugue -i -p -d -u [options]
>>>>>>> fugue -i -p -d -w [options]
>>>>>>> fugue -p -d --saveshift= [options]
>>>>>>>
>>>>>>> Optional arguments (You may optionally specify one or more of):
>>>>>>> -i,--in filename of input volume
>>>>>>> -u,--unwarp apply unwarping and save as filename
>>>>>>> -w,--warp apply forward warp and save as filename
>>>>>>> -p,--phasemap filename for input phase image
>>>>>>> -d,--dwelltoasym set the dwell to asym time ratio
>>>>>>> --dwell set the EPI dwell time per phase-encode line - same as
>>>>>>> echo spacing - (sec)
>>>>>>> --asym set the fieldmap asymmetric spin echo time (sec)
>>>>>>> --savefmap filename for saving fieldmap (rad/s)
>>>>>>> --loadfmap filename for loading fieldmap (rad/s)
>>>>>>> --saveshift filename for saving pixel shift volume
>>>>>>> --loadshift filename for reading pixel shift volume
>>>>>>> -m,--median apply 2D median filtering
>>>>>>> --despike apply a 2D de-spiking filter
>>>>>>> --nofill do not apply gap-filling measure to the fieldmap
>>>>>>> --noextend do not apply rigid-body extrapolation to the fieldmap
>>>>>>> --smooth2 apply 2D Gaussian smoothing of sigma N (in mm)
>>>>>>> -s,--smooth3 apply 3D Gaussian smoothing of sigma N (in mm)
>>>>>>> --poly apply polynomial fitting of order N
>>>>>>> --fourier apply Fourier (sinusoidal) fitting of order N
>>>>>>> --pava apply monotonic enforcement via PAVA
>>>>>>> --despikethreshold specify the threshold for de-spiking
>>>>>>> (default=3.0)
>>>>>>> --unwarpdir specifies direction of warping [x/y/z/x-/y-/z-]
>>>>>>> (default y)
>>>>>>> --phaseconj apply phase conjugate method of unwarping
>>>>>>> --icorr apply intensity correction to unwarping (pixel shift
>>>>>>> method only)
>>>>>>> --icorronly apply intensity correction only (must specify output
>>>>>>> with -u,--unwarp)
>>>>>>> --mask filename for loading valid mask
>>>>>>> --unmaskfmap saves the unmasked fieldmap when using --savefmap
>>>>>>> --unmaskshift saves the unmasked shiftmap when using --saveshift
>>>>>>> --nokspace do not use k-space forward warping
>>>>>>> --nocheck turn off all checking
>>>>>>> -v,--verbose switch on diagnostic messages
>>>>>>> -h,--help display this message
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --dwell: Couldn't set_value! valstr="0,00069"!
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> example_func2highres_fieldmaprads2epi_shift
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> example_func2highres_warp
>>>>>>> An error occured while reading file: example_func2highres_warp
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> FM_UD_fmap2epi_shift
>>>>>>> awk: cmd. line:1: BEGIN {print * -1.0}
>>>>>>> awk: cmd. line:1: ^ syntax error
>>>>>>> Cannot open volume FM_UD_fmap2epi_shift for reading!
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> FM_UD_fmap2epi_shift
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>> Image Exception : #22 :: ERROR: Could not open image EF_UD_shift+mag
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>>
>>>>>>> Cannot open sla.png for reading
>>>>>>> Segmentation fault
>>>>>>> rm: nelze odstranit „sl?.png“: Adresář nebo soubor neexistuje
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> ../example_func2highres
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>>
>>>>>>> Cannot open sla.png for reading
>>>>>>> Segmentation fault
>>>>>>>
>>>>>>> Cannot open ../example_func2highres1.png for reading
>>>>>>> Segmentation fault
>>>>>>> /bin/rm: nelze odstranit „../example_func2highres1.png“: Adresář nebo
>>>>>>> soubor neexistuje
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> ../example_func2highres
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> ../example_func2highres
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>> whirlgif Rev 3.04 (c) 1997-1999 by Hans Dinsen-Hansen
>>>>>>> (c) 1995-1996 by Kevin Kadow
>>>>>>> (c) 1990-1993 by Mark Podlipec
>>>>>>> Processed 2 files.
>>>>>>> Image Exception : #22 :: ERROR: Could not open image
>>>>>>> example_func2highres
>>>>>>> terminate called after throwing an instance of
>>>>>>> 'RBD_COMMON::BaseException'
>>>>>>> Aborted
>>>>>>>
>>>>>>> Cannot open sla.png for reading
>>>>>>> Segmentation fault
>>>>>>>
>>>>>>> Cannot open example_func2highres1.png for reading
>>>>>>> Segmentation fault
>>>>>>> /bin/rm: nelze odstranit „example_func2highres1.png“: Adresář nebo
>>>>>>> soubor neexistuje
>>>>>>>
>>>>>>>
>>>>>>> Kind regards
>>>>>>>
>>>>>>> Pavel Hok
>>>>>>> --
>>>>>>> FMRI Lab Olomouc, Czech Republic
>>>>>>> Faculty of Medicine and Dentistry, Palacky University Olomouc
>>>>>>> University Hospital Olomouc
>>>>>>> Olomouc, Czech Republic
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Pavel Hok
>>>> -----------------------------------------
>>>> -- pavelhok.ic.cz <http://pavelhok.ic.cz/>
>>>> -- webdesign a překlady
>>>> -- tel.: 731 702 547
>>>> -- mail.: [log in to unmask]
>>>> -----------------------------------------
>>>>
>>>
>>> Pavel Hok
>>> --
>>> FMRI Lab Olomouc, Czech Republic
>>> Faculty of Medicine and Dentistry, Palacky University Olomouc
>>> University Hospital Olomouc
>>> Olomouc, Czech Republic
>>> fmri.upol.cz <http://fmri.upol.cz/>
>>>
>>
>
>
>
> --
> Pavel Hok
> -----------------------------------------
> -- pavelhok.ic.cz <http://pavelhok.ic.cz/>
> -- webdesign a překlady
> -- tel.: 731 702 547
> -- mail.: [log in to unmask]
> -----------------------------------------
