p{margin:0;padding:0;}
Hello,
I'm a FreeSurfer beginner and would like to ask a question about Choi's
stratium parcellations. I was doing a research to incoorporate the
parcellations by Choi on my subjects' images to delve further to understand the
distincitve characteristics of each parcels.
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c
Hi Sooyun,
To convert the Choi's parcellation to the MNI152 template from FSL, you
should just use mri_vol2vol, rather than FIRST. The command is as follows: "
mri_vol2vol --mov original_choi_MNI152_parcellation.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
FSL_cho
Hi,
I am unable to download free surfer. Is there a problem at the ftp?
Thank you,
Peter
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Hi,
I am unable to download freesurfer. Is there a problem at the ftp?
Thank you,
Peter
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To add to what Thomas said, I would use mri_label2vol whenever
transferring segmentations or labels. In this case, probably it won't
make much difference.
doug
On 01/27/2014 05:49 AM, Thomas Yeo wrote:
> Hi Sooyun,
>
> To convert the Choi's parcellation to the MNI152 template from FSL,
> you
Hi,
We followed the instructions on this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#Masking
to perform diffusion analysis and wanted to ask if there is an option to
view the color-map in addition to the FA and ADC maps ?
We want to make sure that left-right tracts are red
If you want to use GRF, you should use smooth by twice the native voxel
size. I would not go higher than .01 on the threshold
doug
On 01/26/2014 12:52 PM, Susan Ruiz wrote:
> Hi FreeSurfers,
> I was just reading this post to the archive (below) regarding using
> mri_glmfit-sim
> on volume dat
On 01/24/2014 11:54 AM, Natasha Haris wrote:
> Dear Freesurfers,
>
> I am slightly confused about the monte carlo simulation.
>
> First off, I only find a blob when I run the p<0.05 threshold level and don't
> see anything else when I run simulations with p less than that. What does
> this mean?
Hi Peter,
I think this is due to some maintenance the IT folks are doing on some of
the ftp servers. Should be back up by late afternoon (EST).
-Louis
On Mon, 27 Jan 2014, Davis, Peter wrote:
> Hi,
>
> I am unable to download freesurfer. Is there a problem at the ftp?
>
> Thank you,
> Peter
>
Hi,
I am experiencing an issue where I try to save a point in an inflated brain
view and go to the saved point on my brainmask/wm volume and the point is
jumping to a space off of the brain. This happens consistently. Am I doing
something wrong or is this a bug?
Thank you,
Alexander
_
Perhaps try saving it as a txt file directly from excel instead of doing
the cut and paste
On 01/23/2014 08:14 PM, Wanda Truong wrote:
> Hi Doug,
>
> This was all done on a mac. What would be the best way to recreate it?
> Was the above mentioned excel method adequate?
>
> Wanda
>
>
> On 23 Jan
Hi Alexander
do you see any error messages in the terminal window where you started
tksurfer?
Bruce
On Mon, 27 Jan 2014, Denker,
Alexander (NIH/NIMH) [F] wrote:
> Hi,
>
> I am experiencing an issue where I try to save a point in an inflated brain
> view and go to the saved point on my brain
I was strictly using the freeview GUI and not tksurfer so I didn¹t notice
any error messages.
Alexander
On 1/27/14, 12:10 PM, "Bruce Fischl" wrote:
>Hi Alexander
>
>do you see any error messages in the terminal window where you started
>tksurfer?
>
>Bruce
>
>
>On Mon, 27 Jan 2014, Denker,
>Ale
Dear experts!
I installed freesurfer on a machine running Ubuntu 12.04.
I have got some error messages when testing:
~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/be
Would it be possible to share the data that shows this issue? Or does it
happen to any volume you are viewing with freeview?
Ruopeng
On 01/27/2014 12:47 PM, Denker, Alexander (NIH/NIMH) [F] wrote:
> I was strictly using the freeview GUI and not tksurfer so I didn¹t notice
> any error messages.
I think this is a known issue. When you click on the inflated surface,
it uses the xyz for the vertex on the inflated surface. tksurfer uses
the orig or the white. I think it is possible to click on the inflated,
then go to the white (where the cursor should still be at the same
vertex?), the
It seems to be happening with all of our volumes.
On 1/27/14, 1:23 PM, "Ruopeng Wang" wrote:
>Would it be possible to share the data that shows this issue? Or does it
>happen to any volume you are viewing with freeview?
>
>Ruopeng
>
>
>On 01/27/2014 12:47 PM, Denker, Alexander (NIH/NIMH) [F
Dear Experts,
I was wondering if you could possibly help me with a
reviewer-related question:
We conducted a between-group-analysis estimating the
interaction between cortical thickness and age.
In summary, we wanted
to investigate whether the interaction between cortical thickness and age is
Hi all,
I am running surface area analysis in qdec and I get this error:
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS
cmdline mri_glmfit --y
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
--fsgd
/Users/v
Defect-seg is what I was looking for. Thanks Bruce.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Saturday, 25 January 2014 12:36 AM
To: Chris Adamson
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] defect_labels to volume
have you tried mri
All,
Is there any configuration file/source code file that can be edited to display
the reconstruction toolbar by default in tkmedit?
Thank you.
Chris.
Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Research Institute
Royal Chil
Yes, you need to correct over both hemispheres. The way we do this in
FreeSurfer is to first correct over the hemispheres independently. This
gives a cluserwise p-value for each cluster. We then bonferroni correct
across hemispheres, which basically means multiplying the clusterwise
p-value by
Is the disk full?
On 01/27/2014 04:55 PM, Wanda Truong wrote:
> Hi all,
>
> I am running surface area analysis in qdec and I get this error:
>
> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
> cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS
> cmdline mri_glmfit --y
> /Users/vin
Hi Thomas
what format are these in? Can you include extensions in the files you
send in the future?
thanks
Bruce
On Mon, 27 Jan 2014, Thomas Fink wrote:
Hi Bruce,
At the moment we are interested in the volumes and thus we checked and
corrected the aseg-file (corrections done as described in
Pedro Rosa
Hi,
I have a couple of questions about the mris_preproc:
1) Can I include all subjects in the qdec.table, but afterwards exclude some of
them (based on a determined categorial variable) during the statistical
analysis? I understood that the script assembles thickness / area data int
On 01/27/2014 06:03 PM, Pedro Rosa wrote:
>
> Pedro Rosa
>
> Hi,
> I have a couple of questions about the mris_preproc:
> 1) Can I include all subjects in the qdec.table, but afterwards exclude some
> of them (based on a determined categorial variable) during the statistical
> analysis?
I don't
Hi,
1) So I should generate a .mgh file, which will be the input for the
mri_surf2surf script, for each comparison I wish to do?
I have three 3 groups (schizophrenia, bipolar disorder and controls), and both
schizophrenia and bipolar disorder can be further divided into remission /
non-remission
On 01/27/2014 06:28 PM, Pedro Rosa wrote:
> Hi,
> 1) So I should generate a .mgh file, which will be the input for the
> mri_surf2surf script, for each comparison I wish to do?
> I have three 3 groups (schizophrenia, bipolar disorder and controls),
> and both schizophrenia and bipolar disorder c
Hi Folks,
I have two questions related to aparc.a2009s+aseg.mgz:
1. I was wondering if there is a mapping between structures in
aparc+aseg.mgz & aparc.a2009s+aseg.mgz ? For example I would like to know
what "isthmuscingulate" in aparc+aseg maps to in aparc.a2009s+aseg.mgz.
2. I could find a lobe
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