Hello, FSL experts,
I am currently running a TBSS analysis upon diffusion MR data from patient groups and a control group. We are using several diffusion measures: namely FA, Radial/Axial Diffusivity, and Mean Diffusivity. I have a number of significant results from contrasts from each of these measures and I would like to deproject the results back into the subject space as outlined by the last step (option 2) in the TBSS user guide (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide).
I have started with FA. Following the commands:
>>fslmaths tbss_FA_tfce_corrp_tstat2 -thr 0.95 grot
>>tbss_deproject grot 2
The process handles the deprojection of the skeleton-space image to the 'all_FA' image following this, it runs into an error, starting with:
>>de-projection done
>>now creating inverse warp fields...
>>/usr/local/fsl/bin/tbss_deproject: line 105: cd: ../FA: No such file or directory
>>/usr/local/fsl/bin/tbss_deproject: line 112: cd: ../FA: No such file or directory
>>list of original images = all_FA grot_to_all_FA mean_FA
>>cat: best.msf: No such file or directory
I have checked for the 'tbss_deproject' script in /usr/local/fsl/bin/ and it is there. I have also tried creating an empty FA directory inside /mytbss/stats/ which had no effect.
There are then a number of very similar (basically identical) errors, probably resulting from the above errors, from different files which it was unable to create:
>>original target =
>>processing all_FA:
>>Image Exception : #22 :: ERROR: Could not open image all_FA_to__warp
>>invwarp: Problem reading warp-file all_FA_to__warp
>>Image Exception : #22 :: ERROR: Could not open image all_FA_to__warp_inv
>>An error occured while reading file: all_FA_to__warp_inv
>>processing grot_to_all_FA:
>>Image Exception : #22 :: ERROR: Could not open image grot_to_all_FA_to__warp
>>invwarp: Problem reading warp-file grot_to_all_FA_to__warp
>>Image Exception : #22 :: ERROR: Could not open image grot_to_all_FA_to__warp_inv
>>An error occured while reading file: grot_to_all_FA_to__warp_inv
>>processing mean_FA:
>>Image Exception : #22 :: ERROR: Could not open image mean_FA_to__warp
>>invwarp: Problem reading warp-file mean_FA_to__warp
>>Image Exception : #22 :: ERROR: Could not open image mean_FA_to__warp_inv
>>An error occured while reading file: mean_FA_to__warp_inv
I have run the first deprojection option ('tbss_deproject grot 1') upon each of my contrasts with no issue, and have been able to open the file and look through each participants' results to ensure this. I'm not very experienced at all with TBSS so this has me stumped.
Appreciate any help or advice!
Rowan.
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