Hi Matthew,
I'm not sure if you received my response from a few days ago, but I was
hoping to follow up with you again regarding our error messages in
tbss_non_FA for a pediatric sample run with the -n flag. We reran the
dataset through TBSS using the -T flag and strangely, we're getting quite
similar results compared to using the -n flag. Is there a reason for this?
I would have expected the results to be much different since it was using
the adult MNI template. Can you help me understand why this would be? We
are curious if we should continue with the analysis or rerun the analysis
using a pediatric template that would be more suitable for this data (age
ranges 5-16). Thanks in advance for your help and we look forward to
hearing from you soon.
Best,
Stephanie Otto
Graduate Student, Cognitive and Brain Sciences Program
Department of Psychology, MSS 414/MS0296
University of Nevada, Reno
[log in to unmask]
On Tue, Apr 2, 2019 at 4:02 AM Matthew Webster <
[log in to unmask]> wrote:
> Hello Stephanie,
> Can you run the following command on your
> system:
>
> ulimit -s
>
> And then modify the script $FSLDIR/bin/tbss_non_FA by adding a line
>
> ulimit -s <double the number returned in the original ulimit -s call>
>
> Directly after the line:
>
> echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog
>
> And see if that fixes the problem?
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> > On 1 Apr 2019, at 22:37, Stephanie Otto <[log in to unmask]> wrote:
> >
> > Greetings FSL experts,
> >
> > I am fairly new to using FSL and am currently running TBSS on one
> pediatric sample (81 subjects) and one adult sample (113 subjects). I've
> completed the TBSS FA analysis and have now moved to the MD, L1, L2, L3
> non-FA analyses. The tbss_non_FA runs perfectly fine for the adults,
> however for the pediatric sample I get the error message pasted below. The
> TBSS for the peds sample was run with the -n flag, but from what I
> understand that shouldn't prevent the non_FA from running. I have scoured
> the email archives and found previous posts regarding this exact error
> message, however when I try any of those solutions it doesn't seem to solve
> the issue and I get the same error message. As suggested in previous
> correspondence, I have triple checked that all of my file names are the
> same and when I run the command $FSLDIR/bin/imglob *_FA.* it returns
> nothing even though there are 81 files in that directory. I'm not really
> sure how else to troubleshoot from here. Any help is much appreciated.
> >
> > HutslerLab-Thing-1:MyTBSS_C Steph$ tbss_non_FA MD
> > using pre-chosen registration target: A_TCD_29099_FA_FA
> > upsampling alternative images into standard space
> > /usr/local/fsl/bin/tbss_non_FA: line 96: /usr/local/fsl/bin/imglob:
> Argument list too long
> > merging all upsampled MD images into single 4D image
> >
> > Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value
> in seconds]
> > -t : concatenate images in time
> > -x : concatenate images in the x direction
> > -y : concatenate images in the y direction
> > -z : concatenate images in the z direction
> > -a : auto-choose: single slices -> volume, volumes -> 4D (time
> series)
> > -tr : concatenate images in time and set the output image tr to the
> final option value
> > Cannot open volume all_MD for reading!
> > projecting all_MD onto mean FA skeleton
> > Image Exception : #22 :: ERROR: Could not open image all_MD
> > libc++abi.dylib: terminating with uncaught exception of type
> RBD_COMMON::BaseException
> > /usr/local/fsl/bin/tbss_non_FA: line 105: 741 Abort trap: 6
> ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh
> mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA
> all_${ALTIM}_skeletonised -a all_$ALTIM
> >
> >
> > Warm regards,
> > Stephanie Otto
> > Graduate Student, Cognitive and Brain Sciences Program
> > Department of Psychology, MSS 414/MS0296
> > University of Nevada, Reno
> > [log in to unmask]
> >
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