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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 >>> --------------------------------------------------------------------------- >>> >