Hi Sujith
at this point it is hard for us to say. You can try it if you like. Something is wrong though if you didn't have sphere.reg files as they have been around since the beginning of recon-all.
cheers Bruce
On Fri, 10 Jan 2014, sujith vijayan wrote:
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.edu wrote:
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.whiteOn 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 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.l og
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 <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 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 <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- 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/