Hi experts,
After segmentation of hippocampal subfields, how to generate statistics of
the subfield regions, such as volume?
Thank you
Wang Kangcheng
Faculty of Psychology, Southwest University, China
Email: kangchengwang0...@gmail.com / wangkangcheng@163.com
Address: No.2 Tian
Hi Melinda
The eleventh column age should be age-at-baseline so it's a time-independent
covariate.
If you have only two time-points then you should use the
vertex-wise lme model with a single random effect for the intercept term:
1-Read your label eg.:
lhcortex =
fs_read_label('freesurfer/
Thanks a lot!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, June 27, 2014 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Right hemispheric white matter mean
you get out whatever you put in
On 06/27/2014 03:32 PM, Alshikho, Mohamad J. wrote:
> One more Question...
> If I used <--seg-erode 1 > then I will have the mean diffusivity (MD) as an
> output of mri_segstats
>
> Is that right?
>
> Thanks,
> Mohamad
>
> -Original Message-
> From: freesur
One more Question...
If I used <--seg-erode 1 > then I will have the mean diffusivity (MD) as an
output of mri_segstats
Is that right?
Thanks,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
Thank you Doug,
This is ammazing!
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, June 27, 2014 3:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc+as
I think that would work, but it maybe more effort than needed. You could
have just run
mri_segstats --seg /aseg.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh --sum fa.stats
And just look at segmentation 41 (RH WM)
Or you could add --segid 41
and only RH WM will appear in
You could create a 2nd wmparc allowing it to fill in the unsegmented
with the closest gyral parcellation, then merge the parcellations into
lobes, then only look at the lobes in the unsegmented region from the
1st wmparc.
or you could also run
mri_annotation2label --subject $subject --hemi $h
Thank you.
Best,
Elisa
Il giorno 27/giu/2014 20:26, "Douglas N Greve"
ha scritto:
>
> #1. not a problem
> #2. yes, delete it
>
> doug
>
> On 06/27/2014 03:41 AM, elisa veronese wrote:
> > Dear FS users,
> >
> > I'm trying the -localGI on a linux Centos machine, but I'm facing some
> > problems:
>
Can I classify this unsegmented white matter into lobes?!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, June 27, 2014 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Free
Hi Fs Experts,
In order to calculate the right hemispheric white matter mean fractional
anisotropy (FA), I did the following:
1. I used " rh.dwhite.ribon.mgz" as input in mri_binaraize to create a
binary mask (I did convert mgz to nii and vice versa)
2. I used mri_segstats --seg /a
#1. not a problem
#2. yes, delete it
doug
On 06/27/2014 03:41 AM, elisa veronese wrote:
> Dear FS users,
>
> I'm trying the -localGI on a linux Centos machine, but I'm facing some
> problems:
> 1. should I worry about the /Warning: Unable to open display
> 'iconic'. You will not be able to di
what do you mean? Do you want to have it labelled as something instead
of being "unsegmented"? wmparc is a gyral segmentation of WM, so away
from a gyrus it does not have much meaning. We semi-arbitrarily set the
threshold to be 5mm. But you can set the number to be something very
large, and a
Hi,
I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I
get an error as follows:
[TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8
Testing for CUDA device:
/usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries:
libcudart.so.5.0: can
Hi Teo,
Yes it does, but you can use the -no-wsgcaatlas flag. You can also try
using gcut which doesn't use an atlas (almost certain).
Link with skullstripping info:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
On Fri, 27 Jun 2014, Teo Gelles wrote:
Hi
Hi Everyone,
I am trying to skullstrip an mri image without using an atlas. Does the
following command use an atlas at any point? If so, is there a way to run
the skullstripping algorithm without using information from an atlas?
recon-all -s bert/ -clean-bm -skullstrip
Thanks.
Teo Gelles
That's great. Thank you.
On Fri, Jun 27, 2014 at 5:05 PM, Shantanu Ghosh <
shant...@nmr.mgh.harvard.edu> wrote:
> Hi Martijn
>
> You can do nterhemispheric comparison as in the following link:
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
> shantanu
>
> On Fri, June 27, 2014 10:39 am, Marti
Hi Martijn
You can do nterhemispheric comparison as in the following link:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
shantanu
On Fri, June 27, 2014 10:39 am, Martijn Steenwijk wrote:
> Dear all,
>
> I would like to vertex-wise compare the left and right hemisphere
> thickness
> in a group o
Dear all,
I would like to vertex-wise compare the left and right hemisphere thickness
in a group of subjects.
Would it be okay to just substract lh.hickness.0.mgh and rh.thickness.0.mgh
(i.e. the files concatenating the thicknesses of all patients), then smooth
and then perform a one sample t tes
Dear Free-surfer Group, I am currently attempting to use the lme
matlab tools for my longitudinal analysis. My dataset consists of two
time-points, and
I am interested in the group by time interaction for my dataset.
I am attempting to follow the wiki instructions, but are finding them hard at
Dear FS users,
I'm trying the -localGI on a linux Centos machine, but I'm facing some
problems:
1. should I worry about the *Warning: Unable to open display 'iconic'. You
will not be able to display graphics on the screen. *?
2. the script asks me if I wan to remove a file (rm: remove regular fil
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