Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table command?
On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com
wrote:
Dear Doug,
I have read this post(
Hi there,
I am using freesurfer on MRI data of children.
In one dataset I have following error appearing, I did not find described
before.
MRISalloc(41043678, 76): could not allocate faces
Cannot allocate memory
Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014
Dear Freesurfers,
In Fischl et al. 1999 it is highlighted, that the topological structure of the
original surface is preserved in the spherical space and due to the nature of a
sphere, computations (distance, area) measures are easy to make.
My question now, concerns the comparability of
Hi Kristina
you need to give us more context. What command is running when you get
that error?
cheers
Bruce
On Mon, 12 May 2014, Mayer Kristina wrote:
Hi there,
I am using freesurfer on MRI data of children.
In one dataset I have following error appearing, I did not find described
Hi Christopher
the spherical mapping usually has on the order of 17-20% distortion in
distances, and the registration is probably significantly more. I'm not
entirely sure what are trying to do, but you can measure the difference in
great circle length between the sphere and sphere.reg to get
Hi Francesca,
Are you trying to run the tkmedit command in the same terminal window you
have sourced freesurfer? You'll need to source freesurfer in any new
terminal window you open before being able to run any freesurfer commands.
It's possible to set it up so that freesurfer is sourced
Thanks Louis!
Yes, I did run tkmedit from the same terminal window I have sourced
freesurfer...
Francesca
2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:
Hi Francesca,
Are you trying to run the tkmedit command in the same terminal window you
have sourced
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table
On 05/12/2014 03:41 AM, amirhossein manzouri wrote:
Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table
For #2 you can get the average with mri_segstats passing the mask with
the --seg command and using --id 1. If the mask is in fsaverage space,
then just apply it to the y.mgh (i,e the input to mri_glmfit passed with
--y). Use the --avgwf option to mri_segstats. This will give you the
average
Hi,
I would like to install Freesurfer, but I have a problem.
I now only have a PC running Windows OS.
So I am wondering if I could use Freesurfer by windows.(say in VMware
Player)
Or should I buy Macintosh or somtehing because of memory problems?
Sorry for my really novice question,
Ikko Kimura
Ok, could you send the entire terminal output?
Thanks.
-Louis
On Mon, 12 May 2014, Francesca Strappini wrote:
Thanks Louis!
Yes, I did run tkmedit from the same terminal window I have sourced
freesurfer...
Francesca
2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke
Hi Martin,
Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new to
this!). Do you mean something like this?
For examining an increase between timepoint 1 and 2, but the same between
timepoint 2 and 3?
fsid fsid-base years years-to-years
Day1 base 0 0.4
Day2
Hello,
I am trying to use bbrestier to take an .annot file of a particular
structure and register it to MNI space. I want to be able to use one of the
FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and
do a fMRI BOLD extraction in FSL in MNI space. Below is the command I
Nathan,
I've run into problems like these before when the fsaverage directory is
read only. This may be behind your permission denied error. Perhaps try
to deconstruct the annotation file into your subjects_dir and do the
bbregister command on your label of interest from there - or just copy the
The immediate problem is with permissions. The bigger problem is what
you are trying to do. To transfer the label, use mri_label2vol and
$FREESURFER_HOME/mni152.register.dat to map aparc+aseg.mgz to mni152
space. But this is not going to work very well because the label is
small. Mixing
Hi all,
I'm trying to run recon-all on some data using one of the hpc clusters at
my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem
but I'm trying to rerun the data with the new version.
I keep getting this error (FreeSurfer's log file is attached here)
regarding the
I think the last contrast should be of the form
1 -1 0 -1 1 0 1 -1 0 -1 1 0
1 0 -1 -1 0 1 1 0 -1 -1 0 1
but I only looked over it briefly so you should double check that it
makes sense. The others look ok
doug
On 05/09/2014 10:44 AM, Khadka, Sabin wrote:
Hi all,
I am trying to run
Hi Douglas,
I don’t receive any emails from anyone, I only receive the the digest which is
what I “reply” to. So I am not sure what you mean by “try responding to the
email that I sent.” This is why I attempted to email you directly as I thought
that is what you were asking for.
I hope to
Hi Freesurfers,
I am doing some analyses for an experiment where paradigm files were
automatically generated by Matlab during stimulus presentation. The script was
designed to make paradigm files for an older version of freesurfer, so the
files only have 2 columns. I am going to adjust these
Thanx Bruce,
I will try out your suggestion and let you know. I think I will get a good
estimate of the degree of metric distortions, because I have a lot of subjects
tested ;-)
If this will not work, or the distortions are to big, I will make use of the
Spline Tool in Freeview manually
Hi Christopher
I don't think you will be able to draw the geodesic distance in the
ribbon in 3D as it will cut across imaging planes unpredictably. If you
want the true within-subject geodesic distance there are tools for doing
this (I think it was part of Mukund Balasubramanian's Ph.D.
Hi Freesurfers,
Does anyone know if it is possible to manually set the brain centroid
during the EM Registration step of the recon-all pipeline. I am using a
non-default atlas, and have discovered that many of my difficulties have
resulted from the brain centroid being incorrectly assigned to
Yes, you can do that as long as you are not using an FIR analysis.
doug
On 05/12/2014 04:56 PM, Emily Boeke wrote:
Hi Freesurfers,
I am doing some analyses for an experiment where paradigm files were
automatically generated by Matlab during stimulus presentation. The script
was designed
Hi FS experts,
I was wondering whether it would be possible to measure the average
cortical thickness at a specific slice (either axial, coronal, or
sagittal). I read in Bruce's paper: Measuring the thickness of the human
cerebral cortex from magnetic resonance images that Measuring the
thickness
As a quick update to this problem, it looks like the wm_mean and gm_mean
are reasonable during the #SkullLTA and #SkullStripping steps. However, wm
mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps.
Could this have anything to do with using a manual talairach alignment in
Hi Panos
it would certainly be possible to make that measurement, but it wouldn't
tell you anything biologically interesting. Why would you want to do such a
thing? It will reflect the (arbitrary) image slice orientation and not the
brain.
cheers
Bruce
On Mon, 12 May 2014,
Hi Christina
it's pretty hard to diagnose from just a handful of slices. I also doubt
that it's a huge underinclusion - probably if you move click on a point
and change to sagittal you'll see it looks less dramatic. In any case, if
you upload a dataset we'll take a look. Alternatively you can
Hi Mark
did you create your own .gca file? If so, why? Does it happen for all your
subjects?
Bruce
On Mon, 12 May 2014, Mark Plantz wrote:
As a quick update to this problem, it looks like the wm_mean and gm_mean are
reasonable
during the #SkullLTA and #SkullStripping steps. However, wm
Yes, I created my own atlas for use with 1-2 year olds. It seems to be
happening for all of the subjects. I am wondering if changing the recon-all
code to load the manual talairach.lta
file for the EM_registration and CA_normalization would possibly fix the
problem. It seems strange that the
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness
changes from the posterior to the anterior side of the brain and vice
versa (the thickness gradient).
Thank you again for your time!
Panos
Hi Panos
it would certainly be possible to make that measurement, but
Dear Bruce,
I was running:
recon-all -autorecon2-cp, after adding control points.
When I then look at the surfaces using tkmedit -surfs or inflated surfaces
using tksurfer, everything seems to fit and I can open every output I like.
Also values for volumes seem reasonable.
Thanks in advance.
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