I think there must be something else wrong because the sphere.reg has to be there. Did you check?
On 01/10/2014 06:08 PM, sujith vijayan wrote: > Is there a slightly earlier stage I could start at, such that I would > not get an error? > > Sujith > > > On Fri, Jan 10, 2014 at 2:42 PM, sujith vijayan <svijay...@gmail.com > <mailto:svijay...@gmail.com>> wrote: > > Hi All, > > I tried the command you suggested Doug (recon-all -s subject > -wmparc -cortparc2 -aparc2aseg). It exits with an error because > it cannot find the lh.sphere.reg file. The command and what is > displayed after the command is executed is pasted below. > > Sujith > > > recon-all -s MG24_SurferOutput -wmparc -cortparc2 -aparc2aseg > > INFO: FreeSurfer build stamps do not match > > Subject Stamp: freesurfer-Linux-centos4-stable-v4.0.5-20081003 > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /Volumes/Bach_III/New_Data/Duplicate > > Actual FREESURFER_HOME /Applications/freesurfer > > -rwxrwxrwx@ 1 sujithvijayan staff 529281 Oct 8 2008 > > /Volumes/Bach_III/New_Data/Duplicate/MG24_SurferOutput/scripts/recon-all.log > > Darwin Sujiths-MacBook-Air.local 13.0.0 Darwin Kernel Version > 13.0.0: Thu Sep 19 22:22:27 PDT 2013; > root:xnu-2422.1.72~6/RELEASE_X86_64 x86_64 > > INFO: current FREESURFER_HOME does not match that of previous > processing. > > Current: /Applications/freesurfer > > Previous: /usr/local/freesurfer/stable4 > > #----------------------------------------- > > #@# Cortical Parc 2 lh Fri Jan 10 14:32:37 EST 2014 > > /Volumes/Bach_III/New_Data/Duplicate/MG24_SurferOutput/scripts > > \n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz > -seed 1234 MG24_SurferOutput lh ../surf/lh.sphere.reg > /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs > ../label/lh.aparc.a2009s.annot > \n > > setting seed for random number generator to 1234 > > using ../mri/aseg.mgz aseg volume to correct midline > > $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ > > $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ > > MRISreadVertexPosition(../surf/lh.sphere.reg): could not open file > ../surf/lh.sphere.reg > > reading atlas from > /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... > > reading color table from GCSA file.... > > average std = 3.9 0.2 using min determinant for regularization = > 0.000 > > 0 singular and 1066 ill-conditioned covariance matrices regularized > > No such file or directory > > mris_ca_label: could not read spherical coordinate system from > ../surf/lh.sphere.reg for MG24_SurferOutput > > No such file or directory > > > > > > On Fri, Jan 10, 2014 at 11:54 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > On 01/10/2014 11:40 AM, sujith vijayan wrote: > > > > Hi All > > > > I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the > > closest grey matter region for electrodes in some human > epileptic > > patients; I have the RAS coordinates of the electrodes. I have a > > couple of questions: > > > > 1) When the electrode (its RAS coordinate) is close to the > midline and > > out of the grey matter it won't give me the closest grey > matter label > > (like wmparc does with the white matter). Is there someway > to get this > > in a principled manner? For example, is there a way to get a > file with > > all the RAS coordinates and the parcellation labels, so I > could find > > the closest neighbor in Matlab? > > > If you make a label file with the surface RAS coordinates of the > electrodes, you can run run mri_label2label specifying the > same subject > as the source and target and --regmethod surface and --paint > and it will > map the points to the closest surface point. > > > > 2) The recons for three subjects were done between 2008 and > 2010 using > > freesurfer. Therefore files like aparc.a2009s+aseg.mgz, > wmparc.mgz, > > lh.aparc.a2009s.annot are missing. Is there a simple way just to > > recreate these set of files (one command would be great, > even if it > > takes a little bit of time)? Or does the entire recon have > to be done > > again? > > > If you have an installation of FS 5.3, you can run > recon-all -s subject -wmparc -cortparc2 -aparc2aseg > I think this will work on a 5.0 folder. I would make a copy of > your > subject before running it. It will regenerate the > aparc+aseg.mgz file > > doug > > > > Thanks, > > > > Sujith > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <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. > > > -- 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
