In the first command, you need to tell recon-all to do something. Eg, if you add -all, it tells it to analyze everything (keeping any manual edits you might have made). You can also try "-make all" and it will attempt to update the results (so it will not re-run any steps if it thinks that re-running it would not make a difference). doug
On 11/08/2012 11:52 AM, Julia Nantes wrote: > Hello, > I am having trouble with the pre-processing step. When I enter the > recon-all <subject-id> command I get an error: > > [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all > -s ms_018 > ERROR: nothing to do > > When I enter 'recon-all -s ms_018 -qcache' I get a long list of output > but I don't think it worked correctly: > > [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all > -s ms_018 -qcache > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 root wheel 87913 Nov 8 10:52 > /Applications/freesurfer/subjects/ms_018/scripts/recon-all.log > Darwin Lisa-Koskis-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue > Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > INFO: current FREESURFER_HOME does not match that of previous processing. > Current: /Applications/freesurfer/ > Previous: /Applications/freesurfer > /Applications/freesurfer/subjects/ms_018/surf > #-------------------------------------------- > #@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012 > INFO: File lh.thickness does not exist! > Skipping creation of smoothed data for lh.thickness > #-------------------------------------------- > #@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012 > INFO: File lh.area does not exist! > Skipping creation of smoothed data for lh.area > #-------------------------------------------- > #@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012 > INFO: File lh.area.pial does not exist! > Skipping creation of smoothed data for lh.area.pial > #-------------------------------------------- > ....etc > recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012 > done > > My goal is to eventually be able to bring up my T1 images with the > qdec application and segment the motor cortex. > When I use the tkmedit command it works correctly (I have converted my > files to .mgz already). > > Do you know if it is a pre-processing error that is preventing me from > getting the qdec application to work with my own brain images? I > cannot open files in qdec currently. > > Many thanks, > Julia > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
