JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  August 2010

FSL August 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: New reorient bvecs option in eddy current correction FSL4.1.6

From:

"Chr. Rossmanith" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 10 Aug 2010 15:55:05 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (289 lines)

Hi,

I had the same problem and added

LC_NUMERIC=en_US.utf8

after the two if-statements at the beginning of the script (the 
environment variable must be set before any printf statement) and 
changed the first line into #!/bin/bash instead of #!/bin/sh. Now 
everything is fine.

Christina


at Am 10.07.2010 07:45, schrieb Jürgen Hänggi:
> Dear Julie
>
> Thanks for the script, but the following error occurred:
>
> [Juergen-Haenggis-MacBook-Pro:~/Desktop/BrainJH/AA_DTI_Mean_bvecs_corr]
> juergenhaenggi% rotate_bvecs data.ecclog bvecs
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.4995408: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.5017641: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7060742: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.4966655: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.5043377: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .7062690: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7123872: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7015723: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0000361: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.6517546: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.2759087: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7062499: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.2057888: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.6777722: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7062448: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .0200911: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7076907: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7063059: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .4246619: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.5655371: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7067837: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .6902956: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.1523492: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7072872: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.6516364: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.2767978: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7060119: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.2890704: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7097987: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.6426971: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .2974168: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7053500: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.6436004: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .5159477: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4846393: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.7062429: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7063169: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.2927261: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.6448729: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7061729: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4747344: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.5246485: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.4714015: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7081611: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.5249728: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .5555290: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.6435715: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.5259654: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7068406: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4716977: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: -.5264857: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7055344: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7084626: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0007776: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7053081: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4735310: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .5268940: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7097598: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4669370: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .5268019: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .4768530: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7027931: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .5272597: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7049607: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7090095: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0098790: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.6311790: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.4269586: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .6474386: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7032988: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7085508: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0567668: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.2891232: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7060451: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .6467938: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .2999711: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7027256: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .6454681: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7132049: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7006687: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0127784: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7087111: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.2853866: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .6455365: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: -.7011614: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7109955: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0461651: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .0407717: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7015888: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .7110705: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7135912: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: -.7002107: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .0182989: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 89: printf: .7047899: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 90: printf: .0097473: invalid
> number
> /Applications/fsl/bin/rotate_bvecs: line 91: printf: .7091357: invalid
> number
> [Juergen-Haenggis-MacBook-Pro:~/Desktop/BrainJH/AA_DTI_Mean_bvecs_corr]
> juergenhaenggi%
>
> The resulting bvecs file contains only zeros. Any idea while these numbers
> should be invalid? The original bvecs file is attached.
>
> Thanks in advance
> Cheers
> Jürgen
>
>
>
> On [DATE], "Julie Absil"<[ADDRESS]>  wrote:
>
>    
>> Dear Jürgen,
>>
>> Here is the bug-fixed version of the rotate_bvecs script.
>> I just corrected 2-3 syntax errors and also changed the path for the mat
>> files because there was also a problem with that.
>> Now the temporary mat files (one rotation matrix for each direction, read
>> in the<ecclogfile>) are copied in the same folder than the original data.
>>
>> You just have to copy the script in the folder fsl/bin/ where the original
>> rotate_bvecs is stored (if you want
>> you can save a backup copy of the original one under another name).
>> Then use it with the normal command
>>
>> rotate_bvecs<ecclogfile>  <bvecs>
>>
>> I also saw that a rotate_bvecs file exists in the file fsl/src/fdt but I
>> think it is not used.
>>
>> Hope that this correction will work !
>> Tell me if there is any problem.
>>
>> Best regards,
>>
>> Julie
>>
>>
>> At 08:57 9/07/2010 +0200, you wrote:
>>      
>>> Hi Julie
>>>
>>> Please, can you send me your bug-fixed version of the rotate_bvecs script.
>>>
>>> Thanks in advance
>>> Best regards
>>> Jürgen
>>>        
>
> ----------------------------------------------------------------------------
> Jürgen Hänggi, Ph.D.
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
> ----------------------------------------------------------------------------
>
>
>    

Top of Message | Previous Page | Permalink

JISCMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


WWW.JISCMAIL.AC.UK

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager