Dear FS experts
I want to perform a 2-sample test on my LGI data using qdec (whole brain
analysis with potential covariates). I already ran the recon-all -s
my_subject_id -qcache -measure pail_lgi command for each of the subjects and
included pial_lgi as measure in the QDEC Design tab.
However
sfully!
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "André Schmidt
[andre.schm...@unibas.ch]
Gesendet: Mittwoch, 14. Dezember 2016 17:40
An: Freesurfer support list
Betreff: Re: [Freesurfer] recon-all -s -localGI
Greve
[gr...@nmr.mgh.harvard.edu]
Gesendet: Mittwoch, 14. Dezember 2016 17:03
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all -s -localGI
What happens if you run getmatlab ?
On 12/14/16 7:14 AM, André Schmidt wrote:
Dear Doug
Thanks again for your help. I think I have added the path t
d.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Gesendet: Mittwoch, 14. Dezember 2016 17:03
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all -s -localGI
What happens if you run getmatlab ?
On 12/14/16 7:14 AM
, I had to add this path to my linux
path: /Applications/MATLAB_R2011b.app/bin/matlab
On 12/13/16 11:16 AM, André Schmidt wrote:
Many thanks for your help. According to your suggestion, I modified the
start.up file in Users/andre/matlab/startup.m (see attached).
However, I got the following erro
#x27;FREESURFER_HOME');
fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;
On 12/13/16 10:10 AM, André Schmidt wrote:
Dear experts
I am trying to compute the local gyrification index but I am not sure how I
have to do the following:
"You will a
Dear experts
I am trying to compute the local gyrification index but I am not sure how I
have to do the following:
"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your
~/matlab/starup.m script."
Can you please quickly help me what I need to type in the terminal to do
Dear FS experts,
Using recon-all I defined 82 regions for a probabilistic tractography analysis.
To address volume differences across regions, I like to normalize the obtained
streamlines by the number of voxels in each regions. Is there an easy way to
count voxels within each of my 82 regions?
r 2015 17:38
An: Freesurfer support list
Betreff: Re: [Freesurfer] cannot start freesurfer from terminal
Hi Andre
what are you expecting to happen? The sourcing just sets a bunch of
environment variables and paths - it doesn't start anything
cheers
Bruce
On Sun, 8 Nov
2015, André Schmidt wrote
Dear FS experts,
Surprisingly, I am no longer able to start freesurfer from the terminal:
Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer
Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
Do you know what I am doing wrong?
Thank you
Andre
___
t the
node coords? The fsaverage subject is already in MNI coords so you can
transform to it I believe (Doug can confirm).
cheers
Bruce
On
Sun, 8 Nov 2015, André Schmidt wrote:
> Hi Bruce,
>
> Thanks for your reply. But where can I find the node coords? So far I only
> have names
oords. Not
sure if we have anything to do this by default - Doug would know
cheers
Bruce
On Sat, 7 Nov 2015,
André Schmidt wrote:
> Dear experts,
>
> I defined 84 regions obtained from the aparc+aseg.mgz file as my nodes for
> later graph analysis. For visualization purposes, I wa
Dear experts,
I defined 84 regions obtained from the aparc+aseg.mgz file as my nodes for
later graph analysis. For visualization purposes, I want to assign each node
the corresponding MNI coordinates. Can you please help me how I can do this? Is
this documented somewhere?
Many thanks for your
Dear FS experts,
I would like to know the MNI coordinates of my ROIs obtained from recon-all
(aparc+aseg.mgz file). For example what for coordinates has number 10 (left
thalamus)? Are the coordinates of each region listed somewhere?
Many thanks for your help
Best wishes
André
Dear FS experts,
I have created some seed files and wanted to ask you if everything is fine with
this procedure.
After using recon-all -subject xy -i xy.nii.gz -all, I labelled my files with
mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o label.nii.gz
Then I used bbregister and mri_label
Dear experts,
I am preparing seeds for a later tractography analysis in fsl (sorry about
this). I am bit concerned about the location of my final seed regions and
wanted to ask you if there is something wrong in my pipeline.
I first started using recon-all -subject HC015 -i HC015.nii.gz -all.
Dear freesurfer experts,
I intend to create ROIs from the aparc+seg.mgz file and would like to ask
whether the following assignments are correct (sorry for the long list):
10: left_thalamus
11: left_caudate
12: left_putamen
13: left_pallidum
17: left_hippocampus
18: left_amygdala
26: left_accumb
ects/HC001/b0_brain.nii.gz
Thanks,
Lee
On Thu, 23 Apr 2015, André Schmidt wrote:
> Dear Lee,
>
> Thanks a lot for your help. Unfortunately, now I've go the following error:
>
> Number of labels: 0
> Annot File: (null)
> Template Volume: b0_brain.nii.gz
> Outut Volume: lef
]
Gesendet: Mittwoch, 15. April 2015 19:04
An: Freesurfer support list
Betreff: Re: [Freesurfer] midbrain mask
oh, if you have no anatomical images then we can't help you
Bruce
On Wed, 15 Apr
2015, André Schmidt wrote:
> Thanks Bruce. I'll try this.
>
> The problem is I hav
ral diencephalon"
On Wed, 15
Apr 2015, André Schmidt wrote:
> Dear FS experts,
> Can you please guide me how to create a binary mask of the left midbrain
> (VTA, SN)?
>
> Thanks for your help
> Andre
>
>
___
Freesurfer
Dear FS experts,
Can you please guide me how to create a binary mask of the left midbrain (VTA,
SN)?
Thanks for your help
Andre
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Th
mand failed without
creating any volume, that the volume was created but it doesn't look
right, etc.
Please send us the command line that you type and all the text that the
command outputs on your terminal window.
a.y
On Tue, 17 Mar 2015, André Schmidt wrote:
> Hi Anatasia,
>
> I
us the command line that you type and all the text that the
command outputs on your terminal window.
a.y
On Tue, 17 Mar 2015, André Schmidt wrote:
> Hi Anatasia,
>
> I was able to create a registration.dat with bbregister now ("bbregister --s
> HC001 --mov HC001/mri/bo_brain
009s.annot as seed masks for tractography
Hi Andre - What do you mean by diffusion file? The registration file that
transforms between diffusion and anatomical space is output by bbregister
(see part A of the tutorial that I mentioned below).
a.y
On Tue, 17 Mar 2015, André Schmidt wrote:
> Hi
the multimodal integration tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
a.y
On Thu, 26 Feb 2015, André Schmidt wrote:
> Hi Anastasia,
>
> Thank you very much for your help. I have created such a label nii file, for
> example for ID 9, the left t
that label into DWI space. We recommend bbregister
for the cross-modal registration.
a.y
On Thu, 26 Feb 2015, André Schmidt wrote:
> Dear freesurfer experts,
> I intend to use the aparc.a2009s.annot file as seed regions for a
> tractography analysis. I like to compute streamlines betwee
pport list
Betreff: Re: [Freesurfer] recon-all and subcortical regions
Hi Andre
if you ran recon-all you will have created a volume file names aseg.mgz
that has the subcortical segmentation (and an aparc+aseg.mgz that has
both subcortical and cortical in it)
cheers
Bruce
On Thu, 26 Feb 2015, André Sch
Dear experts,
I use recon-all for the parcellation of my MPRAGE. As far as I can see this
procedure does not address subcortical regions - right? How can I additionally
perform a parcellation of subcortical regions?
Many thanks for your help
Andre
___
Dear freesurfer experts,
I intend to use the aparc.a2009s.annot file as seed regions for a tractography
analysis. I like to compute streamlines between every region in the annot file.
Can you please guide me how I can create masks for every region in the annot
file (or a text file with all seed
Dear experts,
How many regions are included in the apart.annot and apart.a2009s.annot files,
and which one do you recommend for later tractography analysis (using these
regions as seeds)?
Thank you
BW
Andre
___
Freesurfer mailing list
Freesurfer@nmr.m
Dear free surfer experts,
I intend to do a parcellation on my mprage images. The purpose of that is to
use them further as seeds for tractography analysis. So far I used recon-all as
follows:
recon-all -subject xy -i xy.nii.gz -all
But this is quite time-consuming and I want to ask for the com
mgh.harvard.edu
Betreff: Re: [Freesurfer] tksurfer
Is it world readable? You might also change its name to license.txt
On 2/3/15 12:13 PM, André Schmidt wrote:
Dear experts,
I like to see the obtained annotation files using tksurfer. However, I already
got the following error message if I use tks
Dear experts,
I like to see the obtained annotation files using tksurfer. However, I already
got the following error message if I use tksurfer HC001 lh inflated in the
terminal:
FreeSurfer license file /Applications/freesurfer/.license not found
But there is a .license file in that folder.
Ca
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