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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