Re: [Freesurfer] Process flow: ReconAllDevTable

Hi Nick I have a followup question about Scenario D:

Scenario D (for pial edits): 1. recon-all -s <subject> -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s <subject> -autorecon-pial

I think -autorecon-pial is a subset of -autorecon3 ? Is so then could i still run -autorecon-pial without running -autorecon3? Or if i did this would i miss some of the outputs generated by -autorecon3.

Also if -autorecon-pial is a subset of autorecon3, is the following scenario valid. Scenario E (for pial edits): 1. recon-all -s <subject> -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s <subject> *-autorecon3 (instead of -autorecon-pial)*

Thanks Mehul

On Wed, Mar 13, 2013 at 12:31 PM, Mehul Sampat mpsampat@gmail.com wrote:

Hi Nick, Thank you very much. I have two followup questions. Since Scenario B is permissible, I believe the following two scenarios should also be allowed. (Just wanted to confirm this:)

Scenario C (for white matter edits):

1. recon-all -s <subject> -autorecon1 -autorecon2
2. edit wm.mgz (

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) 3. recon-all -s <subject> -autorecon2-wm -autorecon3

Scenario D (for pial edits):

1. recon-all -s <subject> -autorecon1 -autorecon2
2. edit brainmask.mgz (

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s <subject> -autorecon2-pial

Basically, I am trying to see if I can avoid running -autorecon3 in the first run; make all the edits and then re-run recon-all with appropriate flags.

Thanks Mehul

On Wed, Mar 13, 2013 at 10:58 AM, Nick Schmansky < nicks@nmr.mgh.harvard.edu> wrote:

...

Mehul,

Scenerio B is permissible. And to address your question, the pial surface is created in the autorecon3 stage, making use of the parcellation data to refine it. I think a pial is generated during make_final_surfaces as its normal output, but its overwritten in autorecon3.

Nick

On Wed, 2013-03-13 at 10:52 -0700, Mehul Sampat wrote:

...

ps: just wanted to add a clarification to my question. The two scenarios are: Scenario A:

1. recon-all -s <subject> -autorecon1 -autorecon2 -autorecon3
2. add control points
3. recon -all -s <subject> -autorecon2-cp -autorecon3

Scenario B:

1. recon-all -s <subject> -autorecon1 -autorecon2
2. add control points
3. recon -all -s <subject> -autorecon2-cp -autorecon3

If Scenario B is permissible, the advantage is that, -autorecon3 is only run once thus saving a few hours of computation.

Thanks Mehul

On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat mpsampat@gmail.com wrote: Hi Folks, Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then run -autorecon2-cp and -autorecon3 again.

    Recently, I was looking at the process flow table:
    http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
    and I have two questions:


    1. From this table it seems like ?h.white is created in
    autorecon2 and ?h.pial is created in autorecon3.
    However, when i run recon-all -s subj -autorecon1 -autorecon2
    i see that ?h.pial is also already created.
    Does this mean I am interpreting the process flow table
    incorrectly or is there an error in the table ?


    2. Also if ?h.pial and ?h.white are already created at the end
    of autorecon2; then  can we add control
    points at immediately after autorecon2 ? This way we would
    need to run autorecon3 only once and save resources.


    Or am I missing something and is it that one must run
    -autorecon2 and -autorecon3 and then add control points
    and then run -autorecon2-cp and -autorecon3 again.


    Thanks
    Mehul

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