Hi there,
I've run autorecon2 on a subject who has significant unilateral
atrophy in the anterior temporal region. In the last few slices
anteriorly, the pial surface does not include what is clearly
atrophied cortical tissue without underlying white matter. What is the
method to correct f
Anita,
A required update to the aseg/aparcstats2table utilities was not
included in v4.3.0. You can get it here:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/stats2table.tar.gz
copy this file to your $FREESURFER_HOME/bin, and then type:
gunzip stats2table.tar.gz
Nick
On Tue
Leticia,
In the interim until the new longitudinal stream is released, you can
run all your timepoints through the regular stream (recon-all -all), as
this is required in the new stream. Doing so was not required in the
existing (old) longitudinal stream (only the first timepoint was
required, no
Pedro Paulo,
How much memory does the system have? the mri_ca_register stage is
pretty memory intensive. it needs at least 1GB just for itself.
Nick
On Tue, 2009-05-12 at 18:10 -0400, Bruce Fischl wrote:
> is it repeatable?
> On Tue, 12 May 2009, Pedro Paulo de Magalhães Oliveira
> Junior wro
is it repeatable?
On Tue, 12 May 2009, Pedro Paulo de Magalhães Oliveira
Junior wrote:
I have a researcher here who experienced a crash in Bert dataset, any hints?
-- Forwarded message --
From: João Ricardo Sato
Date: 2009/5/12
Subject: Re: Erro no FS
To: Pedro Paulo de Magalh
We are seeking an RA for a data analysis oriented position. Previous
experience with FreeSurfer FS-FAST and MEG/EEG MNE analysis stream is
highly valued. Ability to use MATLAB for mathematical modeling of fMRI and
MEG/EEG data is required. For details, please see
http://www.nmr.mgh.harvard.edu/ma
Hi Corey,
something is very strange with that volume. Is it really only 77 slices? It
doesn't show properly in tkmedit, which means that the direction cosines
are probably messed up. The voxel sizes may be wrong too, as it looks very
odd. Do you have dicoms for it?
Bruce
On
Tue, 12 May 200
When trying to perform an auto recon on MRI_1.nii in
/space/annecy/12/users/adykstra/cashlab/MRI/BW10/mri/, I get the
following error during autorecon1:
---
Hi Leticia,
the recon-all -long stuff is not quite ready yet. Hopefully we'll have
something to distribute within a week or so.
cheers,
Bruce
On Tue, 12 May 2009
l.gutier...@ion.ucl.ac.uk wrote:
Hi,
We have installed the 4.0.1 version and we are starting the longitudinal
analysis. I have
Hi,
We have installed the 4.0.1 version and we are starting the longitudinal
analysis. I have some problems with -base flag( recon-all -base
-base-insubj -base-insubj ... -all).
Should 4.0.1 version be one problem in order to do that?
Many thanks
Leticia
>
___
Hi all,
version FreeSurfer 4.3.0
Problem:
when I run qdec and I generate Stats Data, I can't import aseg.volume
Command line shows this error:
ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in
/home/anita/freesurfer/subjects/qdec/stats_tables//aseg.volume.stats.dat!
The fa
Thank you, it solved the problem!
Attila
On Tue, May 12, 2009 at 10:46 AM, Bruce Fischl
wrote:
> Hi Attila,
>
> the 2nd part I usually do using setenv in a calling script, and
> $env(ENV_NAME) in tcl. Not elegant, but it works. For the first one I doubt
> it - we usually do this in a shell script
Hi Ali,
it is actually 256 slices. You should be able to convert any of the data
we create back to your original space using
mri_convert -rl 001.mgz
-rl is for "reslice like".
cheers
Bruce
On Tue, 12 May 2009,
Al-Radaideh Ali wrote:
Dear FreeSurfer Experts,
I noticed that the output
Dear FreeSurfer Experts,
I noticed that the output images and even the 001.mgz in orig folder are
re-sliced into 255 slices although my input was 160 slices. Is there any way I
can get the output image with same number of slices? as I need to use the masks
of some structure for further analysi
please unsubscribe me from the list
many thanks,
aza...@liv.ac.uk
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Hi Attila,
the 2nd part I usually do using setenv in a calling script, and
$env(ENV_NAME) in tcl. Not elegant, but it works. For the first one I doubt
it - we usually do this in a shell script and invoke tksurfer once/subject.
cheers,
Bruce
On Tue, 12 May 2009,
Krajcsi Attila wrote:
Hi A
Hi All,
In tksurfer is it possible to change the subject or the hemisphere from the
tcl script we use? I couldn't find the solution for this on the tksurfer
scripting wiki page. Maybe it's not possible. And is it possible to send
parameters from the tksurfer command to the tcl script?
Thank you
Martin,
That etiv number seems high. Does the -tal-check stage pass? did you
rerun the -segstats stage? that calculates etiv.
Nick
On Tue, 2009-05-12 at 15:04 +0200, Martin Kavec wrote:
> Bruce,
>
> but I am running 4.3.0
>
> Thanks,
> Martin
>
> On Tuesday 12 May 2009 14:55:05 Bruce Fisch
Bruce,
but I am running 4.3.0
Thanks,
Martin
On Tuesday 12 May 2009 14:55:05 Bruce Fischl wrote:
> Hi Martin,
>
> I'll leave this for Nick, but we fixed the atlas eTIV calculations in the
> new version. Not sure which step you need to rerun though.
> Bruce
>
_
Hi Martin,
I'll leave this for Nick, but we fixed the atlas eTIV calculations in the
new version. Not sure which step you need to rerun though.
Bruce
On Tue, 12 May 2009, Martin Kavec wrote:
Hi Bruce,
On Tuesday 12 May 2009 13:28:36 Bruce Fischl wrote:
Hi Martin,
there are probably some
Hi Bruce,
On Tuesday 12 May 2009 13:28:36 Bruce Fischl wrote:
> Hi Martin,
>
> there are probably some files it wants to see early in the stream that
> didn't exist in 2006. I think the only cure is to string together the
> individual commands you want to run (you can find them in the recon-all
>
Hi Martin,
there are probably some files it wants to see early in the stream that
didn't exist in 2006. I think the only cure is to string together the
individual commands you want to run (you can find them in the recon-all
help).
cheers,
Bruce
On Tue, 12 May 2009, Martin Kavec wrote:
Hi B
Hi Bruce,
-make all is not really helping; recon-all starts from the beginning. However,
in these subjects I did not run the whole pipeline. In fact, here is what I
did with the subjects: in 2006: recon-all -all, and in 2009:
recon-all -autorecon2 -autorecon3, where the autorecon3 failed. It se
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