Hi Mia, If you don't use recon-all, your log will not be saved in recon.log. You can redirect the output in a text file instead, i.e
mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 6 > mylog.txt Best, Marie On Jun 4, 2014, at 8:22 PM, "Borzello, Mia" <mborze...@partners.org<mailto:mborze...@partners.org>> wrote: Hi Marie, The full command is: mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 6 and mris_compute_lgi --i rh.pial --close_sphere_size 30 --smooth_iters 60 Where can i find the error log? I'm looking in the scripts folder and i see recon-all.log (attached)? Thanks so much, m ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Marie Schaer [marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>] Sent: Wednesday, June 04, 2014 2:09 PM To: Freesurfer support list Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] pial layers Hi Mia, I'm not sure to understand what you mean with pial layers. Recon-all -lgi computes the local gyrification index. Can you please send the full command and full log of the error that you get? Best, Marie On 4 juin 2014, at 19:47, "Borzello, Mia" <mborze...@partners.org<mailto:mborze...@partners.org>> wrote: Hi Freesurfers, I ran mris_compute_lgi to make the pial layers but they've error- I've included a screenshot. It says it can't find that directory, but I'm pretty sure that directly exists. Thanks so much for your help, Mia <freesurfer.PNG> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 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.
