I am experiencing the same problem. I am using Ubuntu 10.10 with
2.6.35-24-generic kernel. FSL version 4.1.6 obtained from NeuroDebian.
fslmaths Finger_stat_map.nii -tfce 2 0.5 6 Finger_stat_map_maths.nii
runs without errors and produces an empty (zero filled image). However, this:
fslmaths Finger_stat_map.nii -mul 10 Finger_stat_map_maths.nii
runs correctly. You can find the file I had problems with, here:
http://dl.dropbox.com/u/412959/Finger_stat_map.nii
Thanks in advance for a quick reply.
Best regards,
Chris
On 19 October 2010 11:41, Matthew Webster <[log in to unmask]> wrote:
> 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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