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 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
<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
>
>
>
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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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