Hi Doug,
Do you think I need to have the whole recon done again? What if I ran recon-all with just autorecon3, would that generate all the necessary files (provided what ever that is needed to that point exists)?
From looking at the documentation it seems like that might do. If that
would work, are there any version compatibility issues I need to worry about?
Thanks, Sujith
On Fri, Jan 10, 2014 at 8:19 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
it is necessary to do the aparc.a2009s. It should not be needed for wmparc (unless other files are not there)
On 1/10/14 8:08 PM, sujith vijayan wrote:
Hi Doug,
These were not done by me. What I have are the electrodes on top of MR images as well as their RAS coordinates (I sent you a screen shot before); done by registering a preop MRI with a postop CT scan. Is sphere.reg necessary for that?
Sujith
On Fri, Jan 10, 2014 at 7:21 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Hmmm, I think the sphere.reg has been there from the first version of FS. If it is not there, then there is something wrong with that recon. Have you used those recons for other purposes?
On 01/10/2014 07:12 PM, sujith vijayan wrote:
Hi Doug,
I double checked. The older recons do not have lh.sphere.reg in their surf folder or anywhere else it appears. The closest looking thing is a file called lh.qsphere.nofix. Pasted below are the contents of the surf directory (there are two columns).
Sujith
lh.afterrh.after
lh.arearh.area
lh.area.midrh.area.mid
lh.area.pialrh.area.pial
lh.beforerh.before
lh.curvrh.curv
lh.curv.pialrh.curv.pial
lh.defect_bordersrh.defect_borders
lh.defect_chullrh.defect_chull
lh.defect_labelsrh.defect_labels
lh.inflatedrh.inflated
lh.inflated.Hrh.inflated.H
lh.inflated.Krh.inflated.K
lh.inflated.nofixrh.inflated.nofix
lh.new_orig_uncorrectedrh.new_orig_uncorrected
lh.new_qsphere_uncorrectedrh.new_qsphere_uncorrected
lh.origrh.orig
lh.orig.nofixrh.orig.nofix
lh.pialrh.pial
lh.qsphere.nofixrh.qsphere.nofix
lh.smoothwmrh.smoothwm
lh.smoothwm.nofixrh.smoothwm.nofix
lh.sulcrh.sulc
lh.thicknessrh.thickness
lh.volumerh.volume
lh.whiterh.white
On Fri, Jan 10, 2014 at 6:11 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 <svijayan9@gmail.com <mailto:svijayan9@gmail.com> <mailto:svijayan9@gmail.com <mailto:svijayan9@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 whatis 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 systemfrom ../surf/lh.sphere.reg for MG24_SurferOutput
No such file or directory On Fri, Jan 10, 2014 at 11:54 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 closestgrey 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> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
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> <mailto: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 greve@nmr.mgh.harvard.edu <mailto:greve@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/-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/