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
