The easy fix is to edit rawfunc2surf-sess and remove the --cortex flag. Alternatively, you could run mri_vol2surf yourself from a script that you write. I've fixed this in version 6 to allow turning off the use of --cortex.
doug On 06/09/2015 05:53 PM, Jackie Lam wrote: > Hi all, > > I’ve recently completed surface reconstruction of macaque brain using > Sebastian Moeller’s pipeline (http://freesurfer.net/fswiki/MonkeyData) > and now I’d like to analyse retinotopic data and display it on the > surface. However, when I try running selx3avg-sess, I get this error: > “ERROR: cannot determine format of > /export01/data/jack/monkey/subjects/MM/session1/bold/011/fmcpr.sm0.self.lh” > > > which might be resulting from this: > > "session1 To Surface ----------------------------- > rawfunc2surf-sess -fwhm 0 -s session1 -d > /export01/data/jack/monkey/subjects/MM -fsd bold -hemi lh -self -nolog > -update -per-run > instem fmcpr > outstem fmcpr.sm0.self.hemi > ------------------------------ > 1/1 session1 > 1/1 session1 011 lh --------- > Mon Jun 8 16:53:10 EDT 2015 > mri_vol2surf --mov > /export01/data/jack/monkey/subjects/MM/session1/bold/masks/brain.nii.gz --reg > /export01/data/jack/monkey/subjects/MM/session1/bold/011/register.dof6.dat > --trgsubject MM --interp nearest --projfrac 0.5 --hemi lh > --o > /export01/data/jack/monkey/subjects/MM/session1/bold/011/masks/brain.self.lh.nii.gz > > --noreshape --cortex > No such file or directory > mri_vol2surf: could not open label file > /export01/data/jack/monkey/subjects/MM/label/lh.cortex.label” > > Is there a work around for this? Or is there a way to generate > lh.cortex.label without aseg.mgz? > > Thanks! > > Jack > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
