Hello,
Can you let me know which version of FSL you are using ( Centos4, Mac OSX, etc)
Many Regards
Matthew
> Hi All,
>
> Just came across a problem with fslmaths -tfce, I used the following comment
>
> fslmaths inputfile -tfce 2 0.5 26 outputfile
>
> and the output is always all zeros, also tried to play around with the
> E, H, and connectivity parameters as well as -odt float but same
> result always.
>
> I uploaded my file with the reference 768449.
>
> Please kindly check and advise.
>
> Best,
> Leo
>
>
> On Tue, Jun 22, 2010 at 1:38 AM, Matthew Webster
> <[log in to unmask]> wrote:
>> Hello!
>> I think I'd need to test the image to make sure - there's a number of conditions that could generate this error..
>>
>> Many Regards
>>
>> Matthew
>>> Clark - thanks a lot!
>>>
>>> Matthew - what do you think?
>>>
>>> Cheers-
>>> Andreas
>>>
>>> ________________________________________
>>> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Clark Johnson [[log in to unmask]]
>>> Gesendet: Montag, 21. Juni 2010 23:52
>>> An: [log in to unmask]
>>> Betreff: Re: [FSL] AW: [FSL] tfce error
>>>
>>> Mathew / Andreas
>>>
>>> This looks like the issue discussed in February both on the list serve )028951) and subsequently off line (have pasted a couple emails below). We never got this working so am interested to hear if something else has developed
>>>
>>> Clark
>>>
>>> Pasted emails from our discussion in February.
>>> ===========
>>> Hello,
>>> I've gone back through the emails I sent you - it looks like I might have made a typo in the correction:
>>>
>>> Can you change the relevant line to:
>>>
>>> tfce(input_volume[t], height_power, size_power, connectivity, 0, input_volume[t].max()/100.0);
>>>
>>> and rebuild/retest fslmaths?
>>>
>>> Many Regards
>>> Matthew
>>>
>>>
>>> Mathew:
>>>
>>> With the very kind support of Michael Hanke we compiled the updated version of fslmaths. Unfortunately, it still generates an error
>>>
>>> The new error is “Segmentation fault”
>>>
>>> Looks like something else in the flsmaths code needs to be changed.
>>>
>>> Clark
>>>
>>>
>>> =================
>>>
>>>
>>> Hi!
>>> Can you replace the line in fslmaths.cc that reads:
>>>
>>> tfce(input_volume[t], height_power, size_power, connectivity, 0, 0);
>>>
>>> with
>>>
>>> tfce(input_volume[t], height_power, size_power, connectivity, 0, input_volume[t].max());
>>>
>>> and then recompile - the new binary should work as intended...
>>>
>>> Many Regards
>>>
>>> Matthew
>>>
>>>
>>> I’ll give it a try.
>>>
>>>
>>>
>>>
>>>
>>> From: Matthew Webster [mailto:[log in to unmask]]
>>> Sent: Tuesday, February 16, 2010 8:02 AM
>>> To: Clark Johnson
>>> Subject: Re: [FSL] fslmaths & tfce option
>>>
>>> Many Thanks,
>>> I can give you a one-line change to fslmaths that will fix this problem, if you're OK with rebuilding the fslmaths binary by hand...
>>>
>>> Many Regards
>>> Matthew
>>>
>>>
>>>
>>> Hi Mathew
>>>
>>> The number is 102509
>>>
>>> Thanks
>>>
>>> Clark
>>>
>>>
>>> From: Matthew Webster [mailto:[log in to unmask]]
>>> Sent: Tuesday, February 16, 2010 6:23 AM
>>> To: Clark Johnson
>>> Subject: Re: [FSL] fslmaths & tfce option
>>>
>>> Hello Clark,
>>> I think I have a solution to this, but I would like to check with your input image:
>>>
>>> Can you upload your image to:
>>>
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>
>>> and let me know the 6-digit reference number?
>>>
>>> Many Regards
>>>
>>> Matthew
>>>
>>>
>>>
>>>
>>> Hi Steve:
>>>
>>> Fslstats output for the tstat1 image:
>>>
>>> -1.77 2.37
>>> -9.77 10.33
>>>
>>> Other info –
>>>
>>> FSL version 4.1.5
>>> OS: Ubuntu 9.10 (64bit)
>>>
>>> As always – thanks to everyone there for the wonderful support
>>>
>>> Clark
>>>
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith
>>> Sent: Monday, February 15, 2010 1:35 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] fslmaths & tfce option
>>>
>>> Hi - you only have one input image - so it can't be that - but presumably there is something wrong with the input. What do you get from:
>>>
>>> fslstats tstat1 -r -R
>>>
>>> fslhd tstat1
>>>
>>> Cheers.
>>>
>>>
>>> On 12 Feb 2010, at 19:03, Clark Johnson wrote:
>>>
>>>
>>>
>>>
>>>
>>> I’m poking around with the tfce option in fslmaths
>>>
>>> fslmaths tstat1 –tfce 2 .5 6 myoutput
>>>
>>> and keep getting the error:
>>>
>>> RBD_COMMON::BaseException
>>>
>>> From the list I see this error occurring when files have different dimensions – but am not making much progress sorting this out.
>>>
>>> I’ve tried:
>>>
>>> • upsampling to the MNI 2mm standard image
>>> • Setting –odt to float
>>> • Another (several other) input image(s)
>>>
>>> Still the same error – this must be obvious and “stupid” but . . .
>>>
>>> What am I missing?
>>>
>>> Clark
>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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
>>> ---------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Andreas Bartsch
>>> Sent: Monday, June 21, 2010 3:03 AM
>>> To: [log in to unmask]
>>> Subject: [FSL] AW: [FSL] AW: [FSL] tfce error
>>>
>>> Hi Matthew,
>>>
>>> thanks. The reference number is
>>> 410828
>>> The file is called zstat1.nii.gz.
>>> However, it is just one example where fslmaths --tfce is failing.
>>> Cheers-
>>> Andreas
>>> ________________________________________
>>> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matthew Webster [[log in to unmask]]
>>> Gesendet: Montag, 21. Juni 2010 10:34
>>> An: [log in to unmask]
>>> Betreff: Re: [FSL] AW: [FSL] tfce error
>>>
>>> Hi,
>>> If you upload the image to:
>>>
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>>
>>> and let us know the 6-digit reference number, we'll be able to have a look at the image.
>>>
>>> Many Regards
>>>
>>> Matthew
>>>
>>>> hi,
>>>>
>>>> ok - fslmaths does always produce the below mentioned error
>>>>
>>>> fslmaths blah -tfce 2 0.5 6 tfce_blah
>>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>>>> Abort trap
>>>>
>>>> with any image i use as blah. i'm running on 10.5.8
>>>> can anyone test this, should i send an example?
>>>> strangely, all other fslmaths functionalities seem fine. and the image do not only contain negative values.
>>>> cheers-
>>>> andreas
>>>> ________________________________________
>>>> Von: Bartsch, Andreas
>>>> Gesendet: Sonntag, 30. Mai 2010 02:55
>>>> An: FSL - FMRIB's Software Library
>>>> Betreff: AW: [FSL] tfce error
>>>>
>>>> nope - certainly not. can show you the file next week.
>>>> see you tomorrow, have a good flight!
>>>> andreas
>>>> ________________________________
>>>> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Stephen Smith [[log in to unmask]]
>>>> Gesendet: Samstag, 29. Mai 2010 23:34
>>>> An: [log in to unmask]
>>>> Betreff: Re: [FSL] tfce error
>>>>
>>>> Urgh! Did it have only negative values?
>>>> See you tomorrow.
>>>> xxx
>>>>
>>>>
>>>> On 29 May 2010, at 22:08, Andreas Bartsch wrote:
>>>>
>>>> hi,
>>>>
>>>> i got the following error:
>>>>
>>>> fslmaths zstat1 -tfce 2 0.5 6 tfce_zstat1
>>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>>>> Abort trap
>>>>
>>>> any ideas?
>>>>
>>>> cheers,
>>>> andreas
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>>> 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]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
>>>> ---------------------------------------------------------------------------
>>>>
>>
>
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