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#Outputdirectoriesandfiles

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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