Hi Nasia - They both have preprocessing steps because recon-all runs on the T1 and trac-all runs on the DWIs, so they preprocess different images.

You cannot skip any of the steps in recon-all and still get a segmentation. The point of the autorecon schemes is mostly to repeat only one part of the processing if you change something in between, not to skip part of the processing entirely.

Best,

a.y

On Sun, 14 Aug 2016, Athanasia Metoki wrote:

Dear Anastasia,

Thank you so much for responding so fast!
I see what you're saying and thank you for your input.

I have one more question if you don't mind taking a moment to respond. I
noticed that both trac-all and recon-all include some preprocessing steps
(eg. motion correction, eddy current correction, skull stripping). How come
and they both have these steps if one is supposed to run both commands? My
understandind is, if someone wants to run TRACULA from scratch, they would
need to run both recon-all (first) and trac-all (second). One would have to
run recon-all in order to get the cortical parcellation and subcortical
segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all in
the mask creation step.

In my case where I have some preprocessed data, is there a particular
-autorecon# command which only does some of the recon steps that would help
me get the cortical parcellation and subcortical segmentation
(mri/aparc+aseg.mgz) file that I am missing?

I understand I may be asking a lot! Once more thank you very much for your
initial response and your time!

Best,
Nasia Metoki


On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

      Hi Athanasia - TRACULA expects certains files named a certain
      way to be
      there at the end of each preprocessing step. These are described
      here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfile
      s

      If you are using pre-existing files, you have to make sure that
      they
      follow the same file/directory naming convention.

      You just run recon-all with the default settings. The aparc+aseg
      is
      created in one of the last steps of recon-all, so all the
      previous steps
      have to run as well.

      Hope this helps!

      a.y

      On Sat, 13 Aug 2016, Athanasia Metoki wrote:

      > Dear Freesurfer Developers,
      >
      > I am fairly new to image analysis and this is the first time I
      use
      > Freesurfer.
      >
      > I have some DTI data and I have already preprocessed them and
      ran bedpostX
      > using FSL. I ran probabilistic tractography on FSL as well to
      get the
      > connectivity between two distinct brain areas.
      >
      > I am also interested in getting the probability distribution
      for the
      > uncinate fasciculi so I am trying to use TRACULA.
      > My question is: Can I use TRCULA without doing preprocessing
      and dedpostX
      > again? If so, will I need to do the cortical parcelation and
      subcortical
      > segmentation with recon-all and get the aparc+aseg.mgz file in
      order to use
      > TRACULA? Which argument would I need to use when I run
      recon-all?
      >
      > Thank you!
      >
      > Athanasia Metoki
      > Psychology Doctoral Student - Brain and Cognitive Sciences
      Program
      > Cognitive Neuroscience Laboratory
      > Temple University
      > Department of Psychology
      > 1701 N 13th St.
      > Philadelphia, PA 19122
      > Email: athanasia.metoki@temple.edu
      >
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