Hi Satra - What you're showing in the screenshots would be consistent with a L-R flip of the gradient directions, which is what my comparison of your gradients to the original Siemens gradients indicated. (Assuming the data was acquired with the standard Siemens 60 gradient directions.)

a.y

On Tue, 2 Jul 2013, Satrajit Ghosh wrote:

hi ay,
i'll look into the orientations a little later tonight, but here is V1
overlaid on FA for preflip and postflip execution of dtifit. 

cheers,

satra


On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

      Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What
      flip4fsl will do is convert it to LAS, and perform the same
      conversion on the gradient table that you provide. This of
      course assumes that dwi_orig.nii.gz and your gradient table are
      consistent as they come out of your custom preprocessing. Is
      there any chance that they're not?

      Looking at the sample data set that you sent me, I can only see
      what came out of your preprocessing and not what went in. I'm
      assuming that this is from the standard Siemens 60 direction
      sequence, and it has 57 directions b/c 3 of them were thrown out
      by your preprocessing. I don't know which directions were thrown
      out obviously, but the first 2 directions in your gradient table
      are:
      -0.99699027939850948 -0.057720153020443053 0.051758263409041924
      0.63287878858184599 0.066164234845749903 0.77141869630019422

      The first two directions in the Siemens 60 direction gradient
      table are:
      1.0000000000  0.0000000000  0.0000000000
      0.5867917880 -0.3765825401 -0.7168409782

      There's not only a small adjustment of the direction but also a
      sign change there. So I'd look into that.

      Let me know if any of my assumptions about your original data is
      wrong.

      a.y

      On Tue, 2 Jul 2013, Satrajit Ghosh wrote:

            hi anastasia,
            i'm trying to debug a seg fault that some folks are
            seeing deep into a
            tracula run.

            process:

            1. feed dicoms to a script that runs DTIPrep and
            outputs a nifti file, bvec,
            bval 

            (among checking for many artifacts, this reduces the
            b=0 volumes to a single
            registered mean volume, runs eddy correction,
            discards bad directions,
            reorients the gradients appropriately and generates
            a report of the quality)

            2. run tracula on this nifti file

            observation:

            when i run fsl/dtifit on the same nifti file + bvec
            + bval, i get the proper
            orientation for eigvec1 lines. however, when i feed
            this into tracula, the
            output of the dtifit step looks terrible - i.e. the
            lines are not oriented
            as how one might expect water to diffuse.

            suspicion:

            although i have not reached the crash yet, i believe
            it might be related to
            this fact that the gradients are not oriented
            properly relative to the
            volume.

            i also suspect that this has something to do with
            the flip4fsl step inside
            tracula, which is possibly unnecessary because fsl
            already likes the input
            files. but it seems this step is encoded quite
            heavily within the trac-all
            scripts. 

            questions: 

            a. is there a quick way to turn the flip4fsl step
            off?
            b. alternatively do you have any suggestions for
            what to do here? 

            the whole point of running through DTIPrep is to
            clean up the data before
            giving it to tracula or other programs, so i would
            really like to keep that
            step.

            cheers,

            satra





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