Dear FreeSurfer experts,
I'm trying to implement the steps you indicate in the Paired Analysis' wiki
site, but I still don't get something:
In this site, you show the next FSGD file:
GroupDescriptorFile 1
Class Main
Variables Age
Input subject1pair Main 30
Input subject2pair Main 40
Input
Postdoctoral Fellow Position on Imaging Genetics of Infants
Job description:
Computation functional anatomy laboratory at National University of
Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and
cognition studies using neuroimaging techniques. Our group is leading a
large-scale lon
Postdoctoral Fellow Position on Imaging Genetics of Infants
Job description:
Computation functional anatomy laboratory at National University of
Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and
cognition studies using neuroimaging techniques. Our group is leading a
large-scale lon
Hi all - I have just posted a tracula software update. This update adds
some new functionality without any changes to any existing functionality,
so you can use it with any analyses you have already done in 5.3.
What's new:
1. Compute measures of head motion, as in our recent paper:
http://www.
Hi Anastasia,
Thanks for the new features! The first one helps me a lot!! When looking
at 2., I realized I had not understood the Avg values in pathstats.byvoxel.
The non-Avg values are just the measures at each of these voxels on the
MAP, ok. But then it says
" The last four entries are the axia
Hi Vincent - That is correct. The average values of FA/MD/RD/AD in
pathstats.byvoxel.txt are averaged over all the sampled paths for that
subject at equivalent positions along the trajectory of the path. Roughly
speaking, if 0<=s<=1 is the arc length along the path, where s=0 is the
starting p
Run mris_preproc with --paired-diff-norm which will then compute
LI = (L-R)/(.5*(L+R))
Note that some people use
LI = (L-R)/(L+R)
If that is what you want, then divide the mris_preproc result by 2
doug
On 12/08/2013 08:45 PM, krista kelly wrote:
> Hello,
>
> I'm analysing interhemispheric d
Hi Aldo, this ok to me.
doug
On 12/09/2013 04:53 AM, Aldo Cordova wrote:
> Dear FreeSurfer experts,
>
> I'm trying to implement the steps you indicate in the Paired Analysis'
> wiki site, but I still don't get something:
> In this site, you show the next FSGD file:
> GroupDescriptorFile 1
> Cla
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other
questions (reposted below):
1) When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
2) I have no idea how
On 12/09/2013 11:53 AM, krista kelly wrote:
> Thanks Doug! I'll try that instead.
>
> Also, do you or anyone else happen to have the answers to my other
> questions (reposted below):
>
> 1) When viewing the results in tksurfer, which color represents "left
> hemisphere is larger" and which repre
Hi Jon, QDEC does not currently allow more than one covariates of
interest. You will have to use the command-line stream (ie,
mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)
doug
On 12/05/2013 02:57 PM, Jon Wieser wrote:
> HI freesurfer experts
>
> I want to do an analysis in qdec wi
thanks doug,
We've run a 2x2 analysis for thickness in Qdec and want the get the average
thickness value for each cluster, for each subject.
How can i get a table of thickness data , for feach subject in the analysis
Jon
- Original Message -
From: "Douglas N Greve"
To: freesurfer@nmr.m
It is in one of the output files. Look for the .dat file in
mri_glmfit-sim --help
On 12/09/2013 03:01 PM, Jon Wieser wrote:
> thanks doug,
>
> We've run a 2x2 analysis for thickness in Qdec and want the get the average
> thickness value for each cluster, for each subject.
> How can i get a table
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
wrote:
>
> On 12/09/2013 11:53 AM, krista kelly wrote:
> > Thanks Doug! I'll try that instead.
> >
> > Also, do you or anyone else happen to have the answers to my other
> > questions (reposted below):
> >
> > 1) When viewing the r
Hi,
I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each participant but I keep getting the following error:
MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness'
has many more faces than vertices!
Probably trying to use a scalar data file as
Hi Krista
the optional last argument for mris_anatomical_stats is a surface name
(not a scalar field over the surface, like the thickness file)
cheers
Bruce
On Mon, 9 Dec 2013, krista kelly wrote:
Hi,
I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each p
I found data for the average thickness all subjects for each cluster, but I
haven't found the individual subject's thickness for each cluster. can you
direct me to that data?
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Monday, December 9,
Hello,
I'm looking for a way to view the Desikan-Killiany atlas. I'd like to open the
file
$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs in
Freeview (or Tkmedit, or similar) and be able to see the segmentations and
segmentation names, as well as pan through all of
which file did you look in? It should have a name like
cache.th20.abs.y.ocn.dat
On 12/09/2013 05:09 PM, Jon Wieser wrote:
> I found data for the average thickness all subjects for each cluster, but I
> haven't found the individual subject's thickness for each cluster. can you
> direct me to th
Dear Freesurfer users,
I have just ran mri-glmfit on cortical thickness data and corrected for
multiple comparisons using Monte Carlo Simulation. I have significant
clusters (cwp < .05), however, when I analyse the average thickness
measures from the xxx.y.ocn.dat file in SPSS, there are no signif
That is the right file to use, and one would expect to see significant
results. Are you sure you are using exactly the same model? If you have
matlab, I can give you some code to do the analysis using the exact
model that mri_glmfit uses.
doug
On 12/9/13 10:43 PM, Sinead Kelly wrote:
D
Do you mean you want to view it in the volume or the surface? If you
want to load it as a volume, you can try using the aparc+aseg.mgz in the
fsaverage folder
doug
On 12/9/13 5:26 PM, Gregg, Brian E. wrote:
Hello,
I'm looking for a way to view the Desikan-Killiany atlas. I'd like to
ope
Dear all,
I run "recon-all -autorecon-pial -s subjects" after editing the pial by
PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all
manual. So I donot know whether I should run the "recon-all -s subjects
-autorecon3" to complete all the 31 stages?
Thanks.
All the best.
Higher than 1mm resolution helps a lot. We use 0.7mm isotropic in the HCP.
Peace,
Matt.
From: "Megha K."
Date: Monday, December 9, 2013 10:23 PM
To:
Subject: [Freesurfer] Occipital cortex segmentation
Dear Sir/Madam,
I am using freesurfer for 3T MRI analysis of visual cortical thickness
Hi Doug,
thank you for your reply. It is unusual as I also get a significant result
in SPSS for a non-significant cluster in mri-glmfit. Just to make sure I am
doing things correctly - I am interpreting each column in the xxx.y.ocn.dat
file as a cluster in the xxx.sig.cluster.summary file (in nume
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