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" <MBORZELLO@partners.orgmailto:MBORZELLO@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Marie Schaer [Marie.Schaer@unige.chmailto:Marie.Schaer@unige.ch] Sent: Wednesday, June 04, 2014 2:09 PM To: Freesurfer support list Cc: freesurfer@nmr.mgh.harvard.edumailto: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" <MBORZELLO@partners.orgmailto:MBORZELLO@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.edumailto: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.edumailto: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.