Dear freesurfers,
I just finished cerebellar segmentation on almost 100 subjects. I have
read the usual checking procedure that should be performed on
freesurfer website. However I wasn't able to find if there is a
specific checking workflow that can be performed when freesurfer is
used for 100 /
Hi Charles,
You could use the snapshots option with the QAtools. Alternatively, you
can use the volume:structure=name_or_value along with the --screenshot
option to take snapshots of just the cerebellum. A little scripting would
be necessary. Eventually this will be integrated with the
Hi Jürgen,
I have never tested these flags in the long stream. It should not hurt
to pass them in the base and in the long. In the long, the talairach
from the base is used anyway, so the -use-mritotal should have no effect
there, but the -nuintens... should.
Best, Martin
On Sat, 2013-01-05 at
Dear FreeSurfers,
My query relates to the aparc stats file in FreeSurfer. Upon the editing
and reconstruction of my subjects I have noticed that the Mean Thickness
for the cortex was missing, i.e., no value was provided despite it being
there before I ran another reconstruction. While this has
Can you send the aparc.stats file in question?
doug
On 01/07/2013 11:44 AM, Deirdre O Shea wrote:
Dear FreeSurfers,
My query relates to the aparc stats file in FreeSurfer. Upon the
editing and reconstruction of my subjects I have noticed that the Mean
Thickness for the cortex was missing,
what was your command line?
On 01/05/2013 01:43 AM, xiangbo_2010 wrote:
Dear doug
Using the command to only obtain the size of volume from every
subject, however, I want to obtain the size of surface area from every
subject, what should I do? thanks!
Bo Xiang
At 2013-01-05
Hi Satra, I don't think we've ever compiled such a thing. Maybe just run
recon-all and then ls -lR :)
doug
On 01/05/2013 02:48 PM, Satrajit Ghosh wrote:
hi folks,
happy new year.
we are trying to create an object model for the freesurfer directory.
is there a function/script in
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer
5.0.0 and trying to use recon-all 5.2 to alleviate some issues with
disappearing white matter. I'm wondering if it is necessary to have Freesurfer
5.2 in order for recon-all 5.2 to work properly?
When
Hi Jon
we'll need more info than that. Can you send us the recon-all.log?
cheers
Bruce
On Mon, 7
Jan 2013, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using
Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues
with
I can see that the command line is not set up to create the mean
cortical thickness, but I don't know why the arguments for the command
are not being set up properly. Did you run mris_anatomical_stats
yourself or did you just run recon-all again? If you ran recon-all, can
you send me your
you can also run it with --debug as the first option. That should be
more enlightening
On 01/07/2013 01:39 PM, Bruce Fischl wrote:
Hi Jon
we'll need more info than that. Can you send us the recon-all.log?
cheers
Bruce
On Mon, 7
Jan 2013, Jonathan Holt wrote:
Hello all,
Having a
thanks doug,
that's what i ended up doing. once i'm done, i might run it by you'll to
make sure i'm not misinterpreting any of the files.
cheers,
satra
On Mon, Jan 7, 2013 at 12:51 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Satra, I don't think we've ever compiled such a thing.
Oh, I see now, you are including -noaseg and that is causing the
problem. Why are you including that?
You can rerun like
recon-all -parcstats -parcstats2 -s subject
and it should regenerate the stats with the mean cortical thickness
doug
On 01/07/2013 02:32 PM, Deirdre O Shea wrote:
sure,
Dear FreeSurfer expert,
I am using Freesurfer version 5.1.0. After I run the QA Tool and check my
data, I am getting 39 outliers or more for each subject. When I look at the
AsegMeans and DefaultAsegMeans files in the QATool library, i see that the
mean values in these file for each anatomical
Log file attached. Will try with debug ASAP.
s_98xx_v5.2.log
Description: Binary data
On Jan 7, 2013, at 1:38 PM, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using
Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some
Hi Jonathan,
you'll need the full FreeSurfer 5.2 install in order to run the
recon-all script from 5.2. Running the 5.2 recon-all script with 5.0
binaries will not work.
Best Martin
On Mon, 2013-01-07 at 13:38 -0500, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2.
Hi,
I am trying to run a Monte Carlo simulation on functional data constrained to a
label using Freesurfer 4.0.1. I did not use Qdec for data analysis.
Looking at a previous post -
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html
- I see that I should: 1)
Hi Susan, mri_glmfit-sim did not exist in 4.X. If you want to use 4.X,
then you'll need to run mri_glmfit with the simulation options. If I
were you, I would install a version of 5.X. You can run the glm and MC
simulations using 5.X on data created by 4.X, just don't rerun recon-all
using 5.X
Carl,
I see that is one of our Mac OS X builds (the toughest to get working),
we'll try to replicate. Thanks for passing along the info.
Nick
On Mon, 2013-01-07 at 15:50 -0500, Carl Anderson wrote:
Hi Everyone,
I did the full install for 5.2 but got the following crash during
Talairach:
This line hidden in the output I think is the reason:
mri_make_uchar: Command not found.
That command was introduced in 5.1, and is used by the talairach stage.
As Martin suggests, a separate v5.2 install is necessary.
Nick
On Mon, 2013-01-07 at 15:40 -0500, Martin Reuter wrote:
Hi Jonathan,
How do you know it is the volume and not surface area? The values will
be whatever are in y.mgh, so if y.mgh has surface area, then the output
will be surface area.
On 01/07/2013 07:38 PM, xiangbo_2...@126.com wrote:
I used the command:
mri_segstats --i y.mgh --slabel fsaverage lh
You need to rerun the -prior and -path steps, without the trainfile set to
anything, so that it uses the default trainfile with the 33 subjects. Do
not set the reinit option, that has nothing to do with this. The reinit
option is used when initialization fails but his hasn't happened here.
Dear Martin
Thanks a lot for your comment
Cheers
Jürgen
On [DATE], Martin Reuter [ADDRESS] wrote:
Hi Jürgen,
I have never tested these flags in the long stream. It should not
hurt
to pass them in the base and in the long. In the long, the talairach
from
the base is used anyway, so the
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