Hi Nick,
Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore.
Cheers, Ed
On 9 May 2012, at 18:53, Nick Schmansky wrote:
can you send the recon-all.log file? does it say why the lh.orig_corrected file wasnt created?
On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote:
Hi,
I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was
recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject.
recon-all stopped and issued the following error:
cp: ../surf/lh.orig_corrected: No such file or directory.
Note that I included the option -no-wsgcaatlas to get a better skullstripping because in the default mode the skulltripping was bad. With this option it looks good. I got the above error regularly for other subjects as well and by including the -no-wsgcaatlas option recon-all finished without error, except for the present case.
Cheers, Ed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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the memory requirements of the topo fixer are quadratic in the convex hull of the largest defect, so check the lh.orig.nofix and see if there is a connection to the skull or the cerebellum. You will probably need to fix it in the wm.mgz
cheers Bruce
On Thu, 10 May 2012, Ed Gronenschild wrote:
Hi Nick,
Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore.
Cheers, Ed
On 9 May 2012, at 18:53, Nick Schmansky wrote:
can you send the recon-all.log file? does it say why the lh.orig_corrected file wasnt created?
On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote:
Hi,
I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was
recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject.
recon-all stopped and issued the following error:
cp: ../surf/lh.orig_corrected: No such file or directory.
Note that I included the option -no-wsgcaatlas to get a better skullstripping because in the default mode the skulltripping was bad. With this option it looks good. I got the above error regularly for other subjects as well and by including the -no-wsgcaatlas option recon-all finished without error, except for the present case.
Cheers, Ed _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Ed Gronenschild