Hi All -
I am having difficulty getting tbss_non_FA to run for MD data. I have run all the FA analyses, using tbss steps 1-4. I've had no problems running any of the FA analyses, or RD or AD analyses, using the DWI2DT files instead of the dtifit files. For each subject that I include, I get the following error message:
/usr/local/fsl/bin/tbss_non_FA: line 91: 30104 Aborted $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w ${f}_FA_to_${best}_warp $postaffine
K0400-0709.DWI2DT_FA
** ERROR (nifti_image_read): failed to find header file for '../MD/K0400-0709.DWI2DT_FA'
** ERROR: nifti_image_open(../MD/K0400-0709.DWI2DT_FA): bad header info
Error: failed to open file ../MD/K0400-0709.DWI2DT_FA
ERROR: Could not open image ../MD/K0400-0709.DWI2DT_FA
Image Exception : #22 :: Failed to read volume ../MD/K0400-0709.DWI2DT_FA
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/tbss_non_FA: line 91: 30108 Aborted
I've checked the original files and header info to make sure the files are ok, and the files are there and in tact.
I am running analyses from my TBSS directory, which also contains my origdata, FA, and MD directories. Below is an example of the files in my origdata directory:
origdata:
D0001-0209.DWI2DT_FA.nii
D0002-0409.DWI2DT_FA.nii
D0003-0409.DWI2DT_FA.nii
I have copied my MD files (e.g., D0001-0209.DWI2DT_MD.nii) into the MD directory, and then named them identical to the files above.
I had read an earlier post that use of FA in the file names while using tbss_non_FA might confuse the script, so I tried just naming the files without FA (e.g., D0001-0209.DWI2DT.nii), but I got the same error.
Any help with this problem would be greatly appreciated, as I'm not sure what to try next. Thanks!
cheers,
kristen
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