Hi Amanda - The final masks used by tracula are derived from the
structural and not the diffusion data, i.e., they are the whole-brain
FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion
space and dilated slightly. It may be that there was something wrong with
the FreeSurfer reconstructions of those subjects (if, for example, the T1
contrast was poorer in part of the brain and the part was not included in
the brain mask), or that there was misregistration between the T1 and
diffusion. You can troubleshoot this by looking at the aparc+aseg in
diffusion space (from the dlabel/diff directory, over the FA map (from the
dmri directory).
If you still have trouble deciding what went wrong, you can upload a zip
file for me with all the directories created by trac-all (dmri, dlabel,
etc) for one of these subjects, here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Best,
a.y
On Thu, 27 Nov 2014, Worker, Amanda wrote:
>
> Dear All,
>
>
> I have run all of the pre-processing steps on my DTI data and as I am
> checking my nodif_brain_mask I have realised that some of the masks have
> become distorted and twisted in some way. I have attached screenshots of
> both the raw data (which looks fine) and the white mask (which is
> distorted). In addition, as I have read that it is important to check the
> dtifit_V1 and dtifit_FA I have also included these in the word document,
> incase this helps.
>
>
> This distortion has occured for approximately a quarter of the subjects that
> I have processed and the rest look good. Please can you let me know if you
> have any ideas about what has gone wrong and how to fix this?
>
>
> Thanks in advance for your help,
>
>
> Amanda
>
>
>
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