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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