Hello all,

When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message:

Skull Stripping

/root/trabajo/freesurfer/subjects/c1prueba/mri

mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz

Mode: T1 normalized volume

Mode: Use the information of atlas (default parms, --help for details)

*********************************************************

The input file is T1.mgz

The output file is brainmask.auto.mgz

If this is incorrect, please exit with CTL-C

ERROR: cannot find /root/trabajo/freesurfer/subjects/c1prueba/mri/T1.mgz

mri_watershed Error: read failed

Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Nov 18 11:05:17 CET 2009

So, when I run the recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization,as the error message says, a T1.mgz is needed.How can I obtain the T1.mgz to be able to run this recon-all. In fact, the only file that is needed to run the recon-all -autorecon1 -autorecon 2 is the 001.mgz,isn't it?

Thanks for your help.

Africa

From: africa_millan@hotmail.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon without normalization
Date: Wed, 18 Nov 2009 11:32:05 +0100

Hello,

When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message:

Skull Stripping

/root/trabajo/freesurfer/subjects/c1prueba/mri

mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz

Mode: T1 normalized volume

Mode: Use the information of atlas (default parms, --help for details)

*********************************************************

The input file is T1.mgz

The output file is brainmask.auto.mgz

If this is incorrect, please exit with CTL-C

ERROR: cannot find /root/trabajo/freesurfer/subjects/c1prueba/mri/T1.mgz

mri_watershed Error: read failed

Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Nov 18 11:05:17 CET 2009

When I open de mri file of the subject, I realize that there is not any T1.mgz file, because freesurfer did not generate it. So the question is, when I run the function recon-all with the -nonormalization flag added, does freesurfer skip the generation of the T1.mgz file?

Thanks for your help,

Africa.

> Date: Tue, 17 Nov 2009 13:25:56 -0500
> From: sita@nmr.mgh.harvard.edu
> To: africa_millan@hotmail.es
> Subject: RE: [Freesurfer] recon without normalization
>
>
>
> Yes, that looks okay. You can also add -autorecon3 flag if you want the
> dataset to go through the whole recon-all stream.
>
> Thanks,
> Sita.
>
>
>
> On Tue, 17 Nov 2009, africa millan wrote:
>
> >
> > Hello Sita,
> >
> >
> >
> > Is this the right way to add the -nonormalization flag to the recon-all function to skip the normalization step during the first recon-all??:
> >
> >
> >
> > "recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization "
> >
> >
> >
> >
> >
> > Thanks for your help!
> >
> >
> >
> > Africa.
> >
> >
> >
> >
> >
> >
> >
> >> Date: Thu, 12 Nov 2009 13:24:54 -0500
> >> From: sita@nmr.mgh.harvard.edu
> >> To: africa_millan@hotmail.es
> >> CC: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] recon without normalization
> >>
> >>
> >>
> >> You can run recon-all with -nonormalization flag, which will skip that
> >> step.
> >>
> >> Sita.
> >>
> >>
> >>
> >> On Thu, 12 Nov 2009, africa millan wrote:
> >>
> >>>
> >>> Hello,
> >>>
> >>>
> >>>
> >>> Another question:If during the first recon-all, freesurfer makes skullstripping and normalization automatically... Is there any way to run the first recon-all without automatic normalization?
> >>>
> >>>
> >>>
> >>> Is it possible?
> >>>
> >>>
> >>>
> >>> Thanks
> >>>
> >>> Af.
> >>>
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