Hello Chris,
I've been able to replicate this behaviour - it looks like there is an issue with the -tfce option ( and it should only be this single option ) in the 4.1.6 version of fslmaths. There are now fslmaths-interim patches for the Centos and OSX FSl distributions available from:
http://www.fmrib.ox.ac.uk/fsldownloads/patches/
For other distributions, modifying the line in fslmaths.cc reading:
tfce(input_volume[t], height_power, size_power, connectivity, 0, input_volume[t].max());
to
tfce(input_volume[t], height_power, size_power, connectivity, 0, 0);
and rebuilding the binary should fix the problem.
Many Regards
Matthew
> 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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