Hi Stefano,
When segmenting 1 mm scans, the position of the internal boundaries between the
hippocampal substructures largely relies on prior knowledge acquired from our
ex vivo training data and summarized in our statistical atlas. For this reason,
volumes of internal subfields (especially GC-
Hi Doug,
Thank you - I have uploaded the files for you.
Eli
From: Eli Johnson
Sent: Friday, 20 January 2017 5:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Cortical volume from masked region
Hi Doug,
Thanks a lot for your help!
I have run these
Hi experts,
How can I download Freesurfer version 6.0? Is there an available URL link?
Thank you,
Aziz
--
Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campu
Please do not forget windows people
John
On Jan 25, 2017 12:45 PM, "Aziz Nanthaamornphong"
wrote:
> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science Program in
Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine
running on Windows 10?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 24
Dear Juan,
I actually followed the guide on the following website in order to make it work
on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
Installing and running FreeSurfer on Windo
Hi,
The binary expects the 5.0 library files, it means it was compiled with ver
5 of the CUDA Toolkit.
You need to download and install the 5.0 Toolkit and then set your
cuda_home env variable accordingly.
Best regards,
--
Shahid.
On Tue, Jan 24, 2017 at 10:41 PM, Jeff Stevenson wrote:
> hi
Hi,
I wanted to do the brain parcellation using Destrieux atlas on quite big
dataset, however it will take too much time. I thought that maybe there
is a way to restrict the number of regions used for parcellation (for me
the most interesting are areas in the temporal lobe), so it will shorten
Hi Katarzyna
sorry, no, that won't work.
cheers
Bruce
On Wed, 25 Jan 2017, Katarzyna Anna Kazimierczak
wrote:
> Hi,
>
> I wanted to do the brain parcellation using Destrieux atlas on quite big
> dataset, however it will take too much time. I thought that maybe there
> is a way to restrict the
Hi Chris,
Thanks for the suggestions. We’ll put them in future update.
Best,
Ruopeng
> On Jan 25, 2017, at 2:54 AM, Chris Adamson wrote:
>
> Freesurfer devs,
>
> Freeview is really nice to use. I have a few more suggestions:
>
> It would be good to have keyboard shortcuts to change the bru
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> Hi experts,
>
> How can I download Freesurfer version 6.0? Is there an available URL link?
>
> Thank you,
> Aziz
> --
>
> Aziz Nanthaamornphong, Ph.D.,
> Chair of Master of Science P
Thank a lot.
Aziz.
On Wed, Jan 25, 2017 at 9:38 PM, Z K wrote:
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote:
> > Hi experts,
> >
> > How can I download Freesurfer version 6.0? Is there an available URL
> link?
> >
> > Tha
Hmm, I did not get an email. Did you put my email address on the upload?
On 1/25/17 4:55 AM, Eli Johnson wrote:
Hi Doug,
Thank you - I have uploaded the files for you.
Eli
*From:* Eli Johnson
*Sent:* Friday, 20 Ja
Yes, I think I got the correct email. Attached is the notification I received
upon upload.
Thanks
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.zip (251.3 MiB)
Here are the people you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In c
Hi there
Does the 6.0 version of Freeview have a way to edit labels on surfaces
similar to how tksurfer allowed us to do this?
Thanks!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
___
Freesurfer mailing l
Hi Trisanna,
There is no straight-forward way to let you edit surface labels but you can try
these steps:
1. Load a volume and a surface.
2. Load the label you want to edit as volume label (ROI).
3. Select the ROI in the layer list to bring up ROI property panel. Click on
“Map to Surface” dropd
Hi,
I'm wondering if it's okay to run some of the analyses within one study on
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us
starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
___
Freesu
thanks! I will give this a shot.
best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jan 25, 2017 at 12:41 PM, Ruopeng Wang
wrote:
> Hi Trisanna,
>
> There is no straight-forward way to let you edit surface labels but you
> can try these st
Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial
in fsaverage space. I manage to transform lh.pial in fsaverage space but
this does not give corresponding points or a way to do point by point
transformation.
I want to do the same with some vertices from lh.pial-outer-smo
Hello Experts!
I am having trouble checking the registration per step 2 of the pet surfer
tutorial: http://freesurfer.net/fswiki/PetSurfer. The line:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
worked just fine but when checking the registration using the line:
tkregist
Hi Dorian
the transform should be by looking up the spherical coordinates on the
sphere.reg for that vertex index and using that to find the corresponding
fsaverage sphere.reg vertex.
cheers
Bruce
On Wed, 25 Jan 2017, Dorian P. wrote:
> Hi, I am trying to find the corresponding coordinate of a
In the terminal output it says that your movable volume is
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN
TOF STATIC 2/2016004A/IM-0001-0001.dcm
not template.nii.gz. In principle, that should be fine, except that
there are spaces in the path
On 01/25/2017 04:3
Just out of curiosity, digging through recon-all finds this section quoted
below, however I thought -cp and -wm started at different spots?:
case "-autorecon2-cp":
case "-autorecon2-noaseg":
case "-autorecon2-wm":
set DoNormalization2 = 1;
set DoSegmentation = 1;
se
Hi Doug,
We will investigate and fix it asap.
Best,
Ruopeng
> On Jan 25, 2017, at 4:13 PM, Douglas Merkitch
> wrote:
>
> Hello,
>
> I think I have encountered a bug in freeview on
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. When I attempt to draw and
> save an ROI label, I get the
Whereever there are spaces in the pathname, add a "\" in front of the space and
try again, e.g. instead of:
tkregisterfv --mov
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN
TOF STATIC 2/2016004A/IM-0001-0001.dcm --reg
/Users/djsandoval/Desktop/Selwyn/M8712799
I received your data but cannot find either
500_lobes_1-in-fs.mgz or lh.mask.mgz
On 01/25/2017 11:32 AM, Eli Johnson wrote:
>
>
> Yes, I think I got the correct email. Attached is the notification I
> received upon upload.
>
> Thanks
> Eli
>
>
> You recently uploaded the following files to the
Hello Freesurfer experts,
>From your wiki page, I understand how to normalize volumes in subject
>diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
Me again,
Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305
space or have they been updated to the MNI152 space?
many thanks!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
___
Free
Thank you Bruce.
I am not that familiar with this process. How can I look the transformation
of a specific vertex index? Is this done still with mri_surf2surf?
Dorian
On Wed, Jan 25, 2017 at 4:50 PM, Bruce Fischl
wrote:
> Hi Dorian
>
> the transform should be by looking up the spherical coordi
Still in 305
On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> Me again,
>
> Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in
> MNI305 space or have they been updated to the MNI152 space?
>
> many thanks!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrat
yes, mri_surf2surf will do it. In some sense there is really only one
surface for each subject/hemisphere, it just lives at different points in
space (which, pial, inflated, sphere.reg). You can always use the
index of a vertex to go from one to the other. If you give us more details
about
You can't easily transform a single vertex. One way to do it is to
create an overlay with your vertex = 1 and all others = 0, then convert
that to fsaverage and see where it lands. The mapping itself is a little
tricky and can result in some unexpected behavior. The first step is to
go through
ps. you can easily create an overlay with
mri_volsynth --template lh.thickness --pdf delta --delta-crsf
yourvertexno 0 0 0 --o delta.mgh
On 01/25/2017 06:34 PM, Douglas N Greve wrote:
> You can't easily transform a single vertex. One way to do it is to
> create an overlay with your vertex = 1 a
thanks Doug!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve
wrote:
> Still in 305
>
>
> On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> > Me again,
> >
> > Are the fsaverage volumetric coordinates in Fre
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