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Hi Paul, Thanks for the suggestions! I played around withe display thresholds and still looks like a binary mask no matter what. I had suspected that my bvecs were the most likely culprit, but I don't see how. I did manually manipulate these files (from a windows computer) to be in the correct order in the 3x62 matrix, so the only thing I can think of is Windows adding its wonderful carriages, but I thought I took steps to avoid this (ending files in a new line, per the advice of the FAQ page on the fsl website). Plus, I figured that if the bvecs were bad, eddy would have failed but it finished and looks like it did a good job on visual inspection. I suppose I will go back and try concatenating them in a different way than before. Thank you for your input! Josh On Tue, 9 Oct 2018 17:06:43 +0100, paul mccarthy <[log in to unmask]> wrote: >Hi Josh, > >I'm guessing that it's not simply a matter of a strange display range >in your image viewer, but it's worth checking that. > >Otherwise, my guess is that the order in the bvecs/bvals files do not >match the volume order of the data. > >Cheers, > >Paul > >On 09/10/2018, Josh Robinson <[log in to unmask]> wrote: >> Yes of course! >> >> dtifit --data=data.nii.gz --out=dtifit --mask=nodif_brain_mask.nii.gz >> --bvecs=bvecs --bvals=bvals --save_tensor >> >> I have also attached copies of the bvals and bvecs files as well as >> screenshots as the inputted nodif_brain_mask and the resulting fa map. >> ***I know the brain mask looks a little funky, we were unable to run topup >> thanks to the acquisition so there is still some distortion in the eddy >> corrected data, but this is not yet for the purposes of data analysis so >> much as it is an attempt at seeing how we can implement the FSL toolbox to >> our data. >> >> Thank you in advance, >> >> Josh >> >> >> >> On Tue, 9 Oct 2018 09:51:16 +0100, paul mccarthy <[log in to unmask]> >> wrote: >> >>>Hi Josh, >>> >>>Can you share the dtifit command you used, and some screenshots of the >>>inputs and the resulting FA map? >>> >>>Cheers, >>>Paul >>> >>>On 08/10/2018, Josh Robinson <[log in to unmask]> wrote: >>>> Hello FSL experts, >>>> >>>> I am trying to run dtifit on my data, and it runs through with no >>>> errors, >>>> but when I open the FA map, it looks like it just returned my brain mask. >>>> I >>>> have seen that others have run into this problem before, but none of the >>>> solutions for them seem to be working here. >>>> >>>> Our acquisition is a little old, and includes getting to two identical >>>> DTI >>>> acquisitions with one b0 and 30 directions each. These scans were >>>> concatenated and run through eddy. The bvals and bvecs files were also >>>> concatenated (in the same order), in a 3x62 matrix, with the 0s >>>> corresponding to the b0s in the data (the last volume of each scan). I >>>> have >>>> made sure these files end with the appropriate carriage, I have checked >>>> my >>>> output data from eddy as well as the brain mask and both look normal, >>>> and >>>> running the data through bedpostx_datacheck returns the following: >>>> >>>> bedpost/data >>>> data_type FLOAT32 >>>> dim1 256 >>>> dim2 256 >>>> dim3 60 >>>> dim4 62 >>>> datatype 16 >>>> pixdim1 0.828000 >>>> pixdim2 0.828000 >>>> pixdim3 2.200000 >>>> pixdim4 1.000000 >>>> cal_max 0.0000 >>>> cal_min 0.0000 >>>> file_type NIFTI-1+ >>>> >>>> bedpost/nodif_brain_mask >>>> data_type INT16 >>>> dim1 256 >>>> dim2 256 >>>> dim3 60 >>>> dim4 1 >>>> datatype 4 >>>> pixdim1 0.828000 >>>> pixdim2 0.828000 >>>> pixdim3 2.200000 >>>> pixdim4 1.000000 >>>> cal_max 1.0000 >>>> cal_min 0.0000 >>>> file_type NIFTI-1+ >>>> >>>> num lines in bedpost/bvals >>>> 1 >>>> num words in bedpost/bvals >>>> 62 >>>> num lines in bedpost/bvecs >>>> 3 >>>> num words in bedpost/bvecs >>>> 186 >>>> >>>> I am wondering if using two scans with the same acquisition is >>>> introducing >>>> this issue? Otherwise my money is on an error being in the bvecs file, >>>> however after running through eddy successfully I don't know what. Any >>>> help >>>> is much appreciated! >>>> >>>> Josh Robinson >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>> >>>######################################################################## >>> >>>To unsubscribe from the FSL list, click the following link: >>>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> >> > >######################################################################## > >To unsubscribe from the FSL list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1