Hello, I am new to Freesurfer and have recently encountered an error when trying to run a qcache on one of my subjects. Below is the error. I would appreciate any advise you can give. Thanks!
Reading source surface reg /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory Linux thalamos 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 26 14:08:56 EDT 2010
Thank you, Briana
Hi,
I have a fully processed data set (recon-all done) and I want to estimate the effects of the gradient-related distortion. I have the distortion as a nonlinear transform x' = x + delta(x,y,z). Is there any easy (recommended) way in freesurfer to apply such a transform to the results? (that is volume, surfaces, thickness, curvatures, etc.)
Thanks!
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
Hi Costin,
no, I don't think so. You'll need to unwarp the data and rerun recon-all.
Sorry Bruce
On Tue, 27 Jul 2010, Costin Tanase wrote:
Hi,
I have a fully processed data set (recon-all done) and I want to estimate the effects of the gradient-related distortion. I have the distortion as a nonlinear transform x' = x + delta(x,y,z). Is there any easy (recommended) way in freesurfer to apply such a transform to the results? (that is volume, surfaces, thickness, curvatures, etc.)
Thanks!
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the quick answer!
What is your opinion about re-using the found control points, brain mask , and white matter edits? (re-using by non-linearly transforming them in the new space, and just re-run auto-recon2/3)
Best Regards,
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
-----Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: -----
To: Costin Tanase costin.tanase@ucdmc.ucdavis.edu From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: 07/27/2010 01:55PM Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [freesurfer] Apply a nonlinear transformation on the processed data
Hi Costin,
no, I don't think so. You'll need to unwarp the data and rerun recon-all.
Sorry Bruce
On Tue, 27 Jul 2010, Costin Tanase wrote:
Hi,
I have a fully processed data set (recon-all done) and I want to estimate the effects of the gradient-related distortion. I have the distortion as a nonlinear transform x' = x + delta(x,y,z). Is there any easy (recommended) way in freesurfer to apply such a transform to the results? (that is volume, surfaces, thickness, curvatures, etc.)
Thanks!
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/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.
you probably shouldn't, as the deformation could move the control points out of the wm On Tue, 27 Jul 2010, Costin Tanase wrote:
Thanks for the quick answer!
What is your opinion about re-using the found control points, brain mask , and white matter edits? (re-using by non-linearly transforming them in the new space, and just re-run auto-recon2/3)
Best Regards,
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
-----Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: -----
To: Costin Tanase costin.tanase@ucdmc.ucdavis.edu From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: 07/27/2010 01:55PM Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [freesurfer] Apply a nonlinear transformation on the processed data
Hi Costin,
no, I don't think so. You'll need to unwarp the data and rerun recon-all.
Sorry Bruce
On Tue, 27 Jul 2010, Costin Tanase wrote:
Hi,
I have a fully processed data set (recon-all done) and I want to estimate the effects of the gradient-related distortion. I have the distortion as a nonlinear transform x' = x + delta(x,y,z). Is there any easy (recommended) way in freesurfer to apply such a transform to the results? (that is volume, surfaces, thickness, curvatures, etc.)
Thanks!
Costin Tanase, PhD, Clinical Specialist UC Davis Imaging Research Center 4701 X St, Sacramento, CA, 95817 tel: 916-703-5097 cel: 412-362-0484
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sounds like you haven't finished running recon-all on this subject. You can try -make all to have it redo what's needed On Tue, 27 Jul 2010, Robustelli, Briana (NIH/NIMH) [F] wrote:
Hello, I am new to Freesurfer and have recently encountered an error when trying to run a qcache on one of my subjects. Below is the error. I would appreciate any advise you can give. Thanks!
Reading source surface reg /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory Linux thalamos 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 26 14:08:56 EDT 2010
Thank you, Briana
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Bruce Fischl -
Costin Tanase -
Robustelli, Briana (NIH/NIMH) [F]