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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