ok,

how do I get a list of all the commands after mrsi_make_surface?

2012/10/24 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Pietro,

I don't think we've setup a pipeline for that yet. You'll need to rerun the individual commands after mris_make_surfaces (including mris_thickness to regenerate the thickness maps)

cheers Bruce

On Wed, 24 Oct 2012, pietro de rossi wrote:

Hi FreeSurfer people,

...

I'm considering editing through direct repositioning in freeview (under tools->reposition surface) for some scans.

After that, do I need to rerun everything through the whole recon-all pipeline? What would be the command line for that?

Thank you very much,

Pietro

-- Pietro De Rossi, MD ------------------------------**------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital,

Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

thanks!

cheers

2012/10/24 Bruce Fischl fischl@nmr.mgh.harvard.edu

look in the recon-all -help output

On Wed, 24 Oct 2012, pietro de rossi wrote:

ok,

...

how do I get a list of all the commands after mrsi_make_surface?

2012/10/24 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Pietro,

  I don't think we've setup a pipeline for that yet. You'll need
  to rerun the individual commands after mris_make_surfaces
  (including mris_thickness to regenerate the thickness maps)

  cheers
  Bruce


  On Wed, 24 Oct 2012, pietro de rossi wrote:

   Hi FreeSurfer people,
  I'm considering editing through direct repositioning in
  freeview (under
  tools->reposition surface) for some scans.

  After that, do I need to rerun everything through the
  whole recon-all
  pipeline? What would be the command line for that?

  Thank you very much,

  Pietro

  --
  Pietro De Rossi, MD
  ------------------------------**-------
  Sapienza Università di Roma, Facoltà di Medicina e
  Psicologia, Dipartimento
  NESMOS (Neuroscienze, Salute Mentale, Organi di Senso),
  Ospedale
  Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

  NESMOS Department (Neurosciences, Mental Health and
  Sensory Functions),

School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Pietro De Rossi, MD ------------------------------**------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA