I think the version of 5.2 that Nick cut was a little out of synch with
some changes I made. Try using this version of mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos4
doug
On 1/24/13 10:14 PM, Johnson, Hans J wrote:
In mri_segstats command line g
In mri_segstats command line generated from autorecon, I get an error that the
option "--euler" is unknown.
== /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all
3667 if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix
Dear Freesurfer Experts,
I would like the mean surface area measures of each cluster i found using
command line (mri_glmfit). I used mri_glmfit for a group comparison in surface
area between a patient group and a healthy control group. I found 4 different
significant clusters (using FDR correcte
those are probably in non-cortical regions like the midline
cheers
Bruce
On Thu, 24 Jan
2013, jm wrote:
> Dears Freesurfer:
>
> We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we
> can see some vertexes with thickness value equal to 0 (thickness=0 mm).
> Could you tell me when
It usually means that it is part of the medial wall where there is no
cortex. For technical reasons we need to have the surface be a closed
surface (like a sphere). That means that there have to be places that
don't have cortex but we still need to represent. In these places
thickness is set to
Dears Freesurfer:
We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we
can see some vertexes with thickness value equal to 0 (thickness=0 mm).
Could you tell me when that value is reported by Freesurfer? what do
(thickness=0) means?
Thanks in advance !!!
<>___
Derin,
the results vary only a tiny bit because of differences in the
talairach_with_skull.lta file, which was created twice, the second time
with aseg info, which would cause the brainmask to vary slightly if run a
second time. the result differences are well below what you would find
with rando
the best option is to download the beta of v5.2 which linked from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes (look for 'Get a
BETA here'). i've confirmed that that atlas is contained in that release.
Nick
> Hi FS experts,
> I read that the current dev version for recon-all i
Mia,
this time it looks like there was plenty of memory, but it exited on a
defect. make sure the wm.mgz looks good (doesnt have stuff outside the
white matter). see the 'topological defects' section of our tutorial for
info on what to look for and how to fix it.
Nick
> Hi freesurfers,
>
> So
Hi Javier, you don't want to use the gammarvar for Cohen's D. Gammavar
is like the standard error (square of the std error). Instead, use
rstd.mgh located in the main glmfit folder. Otherwise, I think your
equation is right. I don't think you can do this with one call to
fscalc. I think you'd n
Hi Ed, the problem is that your covariates are highly correlated. Eg,
column 1 is nearly identical to column 17.
doug
On 01/24/2013 06:36 AM, Ed Gronenschild wrote:
> Hi,
>
> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following
> error message:
>
> ERROR: matrix is ill-conditioned or bad
Hi Tommi and Chris, this is a known bug that has been fixed in dev (and
upcoming 5.2). Can you use the dev version just for this cmd?
doug
On 01/24/2013 12:14 PM, Chris McNorgan wrote:
> Hi Tommi,
> The mkdir error suggests to me that there is some system-level permissions
> thing going on. If
Thank you Rudolph,
what I would like to have as an end product is a list of overlay values
at each vertex of the decimated surface (i.e. I don't want to synthesize
anything into ROIs).
The overlays are all freesurfer-specific (curvature, thickness, LGI,
etc). I cannot recompute these on the ne
Hi Tommi,
The mkdir error suggests to me that there is some system-level permissions
thing going on. If it can't make the directory, then there is no directory into
which fsl can write the refvol.fslregister.nii files, hence the final 2 errors.
From the command line, are you able to navigate to
If you specifically want to project overlays onto 'mris_decimate'd
surfaces, you won't be able to do that. You could, however, generate new
overlays using the decimated surface, if that's helpful, using
'mris_curvature_stats' and feeding it the newly downsampled/demicated
surface as input.
FWI
Hi FS experts,
I read that the current dev version for recon-all is going to be the same
to the 5.2 version, so I started a new project with the dev version (in
CentOS 4).
I have this very strange error that I am unable to interpret, when running
mpr2mni305 in one case the target is specified as
7
Hi Alex and Bruce,
thanks a lot for your help. Will play around with MNE - looks like it
does what I am looking for.
Nicola
On 01/24/2013 07:54 AM, Alexandre Gramfort wrote:
> hi,
>
> what we do with MEG in the MNE package is indeed store downsampled
> overlays (that actually have a temporal di
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