Hi Africa,
even if the script completed I doubt that it would generate reasonable results without intensity normalization. You are better off using the expert options to make it a gentler normalization (e.g. running mri_normalize with -b $n -g $g
where n < 10 (the default) and g < 1. This will limit the # of points taken to be control points
On Wed, 18 Nov 2009, africa millan wrote:
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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