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
<ayend...@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.met...@temple.edu
>
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