Hi Kristen, what's the result of a $FSLDIR/bin/imglob *_FA.* in your FA directory? Cheers, Gwenaëlle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : Kristen Mackiewicz Seghete <[log in to unmask]> À : [log in to unmask] Envoyé le : Jeudi 7 mars 2013 18h36 Objet : [FSL] Problem opening files for tbss_non_FA 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