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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