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_mil...@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: s...@nmr.mgh.harvard.edu
To: africa_mil...@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: s...@nmr.mgh.harvard.edu
To: africa_mil...@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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