Hello Leontine,
there should be a logfile that will give you the error messages for tbss_2_reg. Also FSL 5.0.2 is an old version - I would strongly recommend upgrading to the latest version ( 5.0.8 ).
Kind Regards
Matthew
> Hi,
>
> Working with FSL is new for me and I have a problem, and can't figure out what the problem is.
>
> I'm trying to run tbss for my research. But step 2 isn't working. This is probably why I get errors in step 3 and 4.
> I think my script is correct. I looked at my .tbsslog and it look corrects too. I'm working in fsl/5.0.2.2 and tried to run tbss only with one terminal open.
> Does somebody know what the problem might be?
> This is what I get in my terminal (I have more participants, but then it would be to long to copy here):
>
> Running TBSS_1
> processing {PAT_004}_dtifit_FA
> processing {PAT_020}_dtifit_FA
> Now running "slicesdir" to generate report of all input images
>
> running TBSS_2
> {PAT_004}_dtifit_FA_FA_to_target
> {PAT_020}_dtifit_FA_FA_to_target
> 3137731
>
> running TBSS_3
> using pre-chosen target for registration transforming all FA images into MNI152 space
> ERROR:: cannot find the following warp results:
> {PAT_004}_dtifit_FA_FA_to_target_warp {PAT_020}_dtifit_FA_FA_to_target_warp
> Please wait for registration (fnirt) to finish or re-run registrations
>
> running TBSS_4
> creating skeleton mask using threshold 0.2
> Cannot open volume mean_FA_skeleton for reading!
> creating skeleton distancemap (for use in projection search)
> Cannot open volume mean_FA_mask for reading!
> Image Exception : #22 :: ERROR: Could not open image mean_FA_skeleton_mask_dst
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /cm/shared/apps/fsl/5.0.2.2/bin/tbss_4_prestats: line 96: 20075 Aborted (core dumped) ${FSLDIR}/bin/distancemap -i mean_FA_skeleton_mask_dst -o mean_FA_skeleton_mask_dst
> projecting all FA data onto skeleton
> Image Exception : #22 :: ERROR: Could not open image mean_FA
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /cm/shared/apps/fsl/5.0.2.2/bin/tbss_4_prestats: line 99: 20076 Aborted (core dumped) ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_FA_skeletonised
>
> Thanks in advance!
>
> Kind regards,
> Leontine
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