Hi Fidel & Saad,

Thank you both for the help! Yes, there are two b0s total, both of which are in the concatenated data as the 31st and 62nd volume (they were acquired last for each run), and this is accurately reflected in the bvals and bvecs. Per Fidel's advice, I rewrote both files to use only tabs and again to use only spaces, but still the same problem either way, and both files also had accurate dimensions (3x62 & 1x62). Visually inspecting the data, it looks as expected, with the b0s in the correct place and contrast from volume to volume.

At this point I am thinking it must be an issue with the bvals/bvecs. Could this be an error in initially generating these files? I used dcm2niix, but I have found that using that to convert par/rec files can sometimes be problematic. I then used the linux function to paste those values into one file

paste file1.bvec file2.bvec --delimiters="" | tr -d '\r' > concatenated.bvec

Alternatively, would it perhaps be better to run the two runs I have through eddy separately and concatenate them & align them to each other later? It would be ideal to concatenate them first, but it is looking more and more like this may not be a feasible approach...

Your assistance is much appreciated!

Josh





On Tue, 9 Oct 2018 20:46:39 +0100, Fidel Alfaro Almagro <[log in to unmask]> wrote:

>Hi Josh,
>
>Your bvals/bvecs file does not have a b0 at the beginning. I am not sure if
>that is a problem (probably not), but it wouldn't hurt if you can confirm
>that is really the case (as far as I can see from your bvals, you have 2
>b0s, right?).
>
>More problems: Your bvecs file has 5 lines (it should have 3). Your bvals
>file has 3 lines (it should have one).
>
>More problems: Your bvals file has BOTH tabs and spaces to separate values.
>Not sure if that is a problem, but better be consistent.
>
>One last note: Even though it would be logical to presume that eddy and
>dtifit are consistent in the way that they read bvals and bvecs files, I
>would not make that assumption. Those 2 tools were written by different
>people, so it may not be the case that the same bvals/bvecs are accepted by
>both.
>
>Please, check all these issues and try dtifit again.
>
>Cheers
>
>Also, opening the
>
>El mar., 9 oct. 2018 a las 18:41, Josh Robinson (<
>[log in to unmask]>) escribió:
>
>> 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
>> >>>>
>> >>>>
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