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 > 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 > > 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. > >
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