Hello,
I got this error while trying to generate the stats table on qdec on my own
data:
What I don't understand is for the 1st error, where it says it can't locate
aseg.stats for 240, the aseg.stats file is in subject 240's file.
But what is the reason for the 2nd error?
asegstats2table --mea
Dear Freesurfer experts,
I would like to transform the aparc.annot file into MNI space in order to
map the parcels from this file to the MNI152_T1_1mm atlas. I have tried the
following unsuccessfully:
./mri_label2vol --annot lh.aparc.annot --subject fsaverage --temp
./fsaverage/mri/brainmask.mgz
Hi
I got an error while running selxavg3-sess, "cannot find AFNI command
3dvolreg".(In ubuntu v11.).
Any help would be appreciated.
Hiroyuki
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I have not set path for afni.
After setting the correct path, that runs fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Oya, Hiroyuki (UI
Health Care)
Sent: 30 March 2012 07:53
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfe
Dear all,
I am working with FreeSurfer version 5.10 from 2 months. I am interested in
hippocampus volume measurements and I want to normalize them with the
intracranial volume.
We have scanned about 4 times the same 2 healthy subjects (3T GE HDxt, 8
channel coil). 3D acquisitions were made
Hi Gabriela
it's hard to get a stable ICV measure from only a T1-weighted image,
since you can't really distinguish bone from air. You can use supra
tentorial, but you are testing a slightly different hypothesis (i.e. that
hippocampal volume is changing faster than supratentorial volume).
ch
Note that a bug in the calculation of the supratentorial volume was
recently identified (see archives), so if you want to use that measure
you should get the fixed version of mri_segstats and regenerate the
aseg.stats files.
cheers,
-MH
On Fri, 2012-03-30 at 09:12 -0400, Bruce Fischl wrote:
> Hi
Hello Surfers,
I am trying to do a qdec analysis and I am working with several
hundred subjects. I have my data divided up into different time points
and a discrete factor called time. I would like to look at just time
1, then time 2, then time 3.
I know how to exclude individual scans by right c
Dear freesurfers,
I have a problem in creating masks of the left and right cerebral cortexes.
The message "found 0 values in range" is displayed and an empty mask is
created. This is surprising as I am able to build masks of the right and left
hippocampi and entorhinal cortexes using the same
Freesurfer universe,
I noticed that the newer version of freesurfer does not output a ?h.base.mgh
file, which contains vertices, but no triangular meshes and corresponding gyral
labels from the color look up table.
Question:
1). Why does my cortical labels created using tksurfer correspond to t
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Dear experts
I have just completed all of the steps leading up to overlaying retinotopy
activation on an inflated brain. I have been able to Make a Closed Path, but
unfortunately when I press the Custom Fill nothing happens. Any ideas why this
is the case. I have been using tksurfer-sess -c pol
what is your command line?
On 03/30/2012 12:00 PM, lorenzo pasquini wrote:
> Dear freesurfers,
>
> I have a problem in creating masks of the left and right cerebral
> cortexes. The message "found 0 values in range" is displayed and an
> empty mask is created. This is surprising as I am able to
Did you click inside the area before doing the fill?
On 03/30/2012 01:02 PM, Kiley Seymour wrote:
> Dear experts
>
> I have just completed all of the steps leading up to overlaying
> retinotopy activation on an inflated brain. I have been able to Make a
> Closed Path, but unfortunately when I pr
What do you mean you were unsuccessful?
Try using --reg $FREESURFER_HOME/average/mni152reg.dat instead of --identity
On 03/30/2012 08:06 AM, Yolanda Vives wrote:
> Dear Freesurfer experts,
> I would like to transform the aparc.annot file into MNI space in order
> to map the parcels from this file
Hi Lingqiang, there is nothing set up to do this. You can use the time
courses as you suggest, but this will no remove WM, CSF, etc. Those time
courses are there too, so you can remove them yourself if you want.
doug
On 03/29/2012 03:44 PM, Lingqiang Kong wrote:
> Hi Surfers,
>
> Has anyone done
Dear all,
If I sum up the Gray Matter Volume (GrayVol) in aparc.stats for left (or
right) hemisphere for all the regions, am I expecting that number to be
different from the volume of the Left-Cerebral-Cortex (or
Right-Cerebral-Cortex)?
Am I correct in assuming that Left-Cerebral-Cortex is the sa
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