Hi Katherine - The dlabel/ directory is created during the -prep step, when the structural segmentation gets mapped from T1 to diffusion space. However bedpost may still run fine without the dlabel/ directory. It seems that the problem is fairly early in the -prep step. Any errors there?

Best,

a.y

On Wed, 23 Mar 2016, Katherine Damme wrote:

Hey Anastasia,

Although the bedpost appears to complete properly the dlabel/diff is not being created during the bedp step. I am not sure how or why this error is occurring. That would, it appears, definitely be the cause of the failure. However, I am not getting an error during the prep or the bedpost stage, and so I am still completely lost any advice would be deeply appreciated!

Thank you,

KD

On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Katherine - Do the freesurfer segmentations look ok? What
  about the registration from structural to diffusion? You can
  inspect those quickly with:

  freeview dmri/dtifit_FA.nii.gz
  dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3

  Hope this helps,
  a.y

  On Sun, 3 Jan 2016, Katherine Damme wrote:

        First I should note that using the same scripts I
        completed 52 participants successfully and am
        currently trying to
        batch process the newest 42 participants that are
        only failing at the path level. Upon Visual
        Inspection they all
        appear normal (with the exception of the one
        attached). After carefully comparing a random sample
        of 5 from each
        group images from the files that failed versus the
        files that were successful, I found:

        1. The range of values in the mean_ph1samples in the
        successful ( i.e. -3.00 to 87.30 ) differed from the
        failures
        (i.e. -2 to 17) (the successful samples varied on
        their high end from 50-114 but the failures were on
        the 5-24
        range)
        2. The range of values in the mean_th1samples in the
        successful ( -0.02 to 19.12) differed from the
        failures
        (-0.00267 to 7.176) (the successful samples varied
        on their high end from 19-17 but the failures were
        on the 3-10
        range)
        3. Some, but not all (2/5), mean_S0samples, had a
        abnormal range in successful (0 to 19998.4) compared
        to the
        unsuccessful (0 to 709.96)

        However, I understand that the diffusion units are
        likely arbitrary and not sure these patterns will
        hold in a
        larger sample.

        I know this is a lot of confusing information and so
        in response to your question. After an initial
        inspection
        there are two types of output:
        1. data that appears visually normal with a slightly
        altered range.
          Should I be concerned about the range if all other
        data looks fine?

        2. data that appears visually normal with a normal
        range and bizarre merged files.
          What do you think could be a cause of these odd
        merged files?




        On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki
        <ayendiki@nmr.mgh.harvard.edu> wrote:

              Hi Katherine - Have you looked at any of the
        intermediate images? Do they look normal?

              a.y

              On Mon, 21 Dec 2015, Katherine Damme wrote:

                    Hello Everyone!

                    It looks as though my prep and bedp
        stages completed properly, but the prep stage ends
        in a
                    segmentation
                    errror.

                    See attached and let me know your
        thoughts. I would prefer not to have to redo all
        steps if
                    possible!
                    Thank you!




        The information in this e-mail is intended only for
        the person to whom it is
        addressed. If you believe this e-mail was sent to
        you in error and the e-mail
        contains patient information, please contact the
        Partners Compliance HelpLine at
        http://www.partners.org/complianceline . If the
        e-mail was sent to you in error
        but does not contain patient information, please
        contact the sender and properly
        dispose of the e-mail.