,
--
Vy Dinh
MD Candidate, Class of 2017
University of Wisconsin School of Medicine and Public Health
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail
wrote:
Use -t hemi.volume (and change the name of the output file:-)
doug
On 10/14/14 2:30 PM, Vy Dinh wrote:
Dear experts,
Can one use mri_anatomical_stats to extract volume information? I have a
set of labels that has been mapped to each subject's native space (using
mri_label2label
crashing when I
click on the configure overlay) and tksurfer.
Ideally, I want to save clusters from the group comparison as a .label
file, so please let me know if there is any free surfer command that can do
this.
--
Vy Dinh
MD Candidate, Class of 2017
University of Wisconsin School of Medicine
using the --label option)? What kinds of things can I
do to run the monte carlo simulation appropriately?
Thank you,
Vy Dinh
MD Candidate, Class of 2017
University of Wisconsin School of Medicine and Public Health
___
Freesurfer mailing list
Freesurfer
with FDR-corrected value?
Thanks in advance,
--
Vy Dinh
MD Candidate, Class of 2017
University of Wisconsin School of Medicine and Public Health
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo
to reflect the new
fsaverages, or write new data? Are there any special steps that I need to
take with respect this change when conducting group comparisons in qdec?
Thank you,
Vy
--
Vy Dinh
MD Candidate, Class of 2017
University of Wisconsin School of Medicine and Public Health
*%* of a single core, so the
programs running off the server should be able to utilize its maximum speed.
I am working closely with our server expert to troubleshoot this issue, so
any insight from the development team will be much appreciated. Thank you.
Best regards,
Vy Dinh
MD Candidate, Class of 2017
Gschwind markus.gschw...@gmail.com
wrote:
Hi!
Can the connection be slow?
Can you type in your local terminal and also in the ssh remote terminal
the following:
glxgears
and let it run a while and past here the output.
Cheers!
Markus
2014-06-03 23:16 GMT+02:00 Vy Dinh vdi...@wisc.edu
Was wondering if anyone from the Freesurfer team is looking into this issue
yet.
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh vy_d...@rush.edu wrote:
BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh vy_d...@rush.edu
cannot say more right now without knowing what you did.
Best, Martin
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh vy_d...@rush.edu wrote:
BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh vy_d...@rush.edu wrote
did.
Best, Martin
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh
vy_d...@rush.edu wrote:
BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013
figure out why the pial surface extends to
include nonbrain regions when recreating the surfaces? *
*
*
*What solutions would you suggest in resolving this problem?*
*
*
Thank you,
Vy Dinh
Research Associate
Department of Neurological Sciences
Rush University Medical Center
BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh vy_d...@rush.edu wrote:
Dear Developers,
I have a significant problem when rerunning the pial edits for the
longitudinal data. Our dataset consists of subjects
Dear Freesurfer Experts,
I would like to create ROIs for the MNI152 template using coordinates
obtained from our QDEC Monte Carlo Simulations results. However, the QDEC
results only list the Talairach Coordinates. Is there a program that I can
use to convert these tal coordinates to MNI152?
Dear surfers,
I'm having trouble downloading the longitudinal data form the website. This
is the command I used:
curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz
Error message:
curl: (56) FTP response reading failed
Am I typing the filename in wrong? Also, I tested the
Dear Freesurfer Experts,
I've created a couple of ROIs from qdec comparisons of thickness and volume
between two groups. We extracted the data from these ROIs for each subject
using mris_anatomical_stats.
The stat files are located within each subjects folder:
sub/stats/rh.roi.stats
Now, we
read the appropriate lines to a single text file
with .
-
Josh
On Thu, May 17, 2012 at 1:04 PM, Vy Dinh vy_d...@rush.edu wrote:
Dear Freesurfer Experts,
I've created a couple of ROIs from qdec comparisons of thickness and
volume
between two groups. We extracted the data from these ROIs
Department of Psychology
University of California, Davis
530.747.3805
On Thu, May 17, 2012 at 2:37 PM, Vy Dinh vy_d...@rush.edu wrote:
Thanks for the suggestion Josh! I have definitely thought about this, but
since I'm a total novice bash programmer, I thought that it would be
quicker
to learn
Dear Experts,
Is it possible to link the four panel display so that as we are scrolling
through each slice in one view, the other three views will automatically
scroll to the next slice (without having the user click the cursor on a new
point)? This was possible in SPM Display tool, so I wonder
Dear forum,
Has anyone else come across this issue and resolved it? If I try to switch the
main volume (after editing the vol), Tkmedit crashes with the following error
message:
% Bus error
It happens no matter what image I select and only when I try to load a new main
volume (not aux
Player [astev...@nmr.mgh.harvard.edu]
Sent: Friday, January 13, 2012 3:55 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.gold...@gmail.com
Subject: RE: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data
and recreating cerebellum in brainmask
Haven't noticed
Dear Freesurfer experts,
We are about to do a mass reprocessing in our lab to update our FS 5.0 data to
the FS 5.1 and would like to do the following all in one run:
1) Preserve the wm and pial edits made in the 5.0 data in 5.1
From our understanding, using the command
Dear Experts,
I've read that the latest Freesurfer release, v5.1, allows one to rerun the
skullstripping step to remove extra dura. This would be a godsend for us since
most pial surface corrections involve removing the dura. However, we have been
using v5.0, which does not have this feature.
Dear experts,
We have recently encountered processing errors (during recon-all and
-autorecon23) due to the creation of symbolic links within our SUBJECTS_DIR.
Since our data were located on a data mount, the system somehow could not
source the linked file. We have addressed this issue by
. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
From: Nick Schmansky [ni...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 02, 2011 3:13 PM
To: Vy Dinh
Cc
Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2
autorecon3
So the BA labels don't exist in
$FREESURFER_HOME/subjects/fsaverage/label? What version are you using?
doug
Vy Dinh wrote:
You're absolutely right. The lh.BA1.label file
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, October 21, 2011 12:22 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2
autorecon3
The BA labels should be in
$FREESURFER_HOME/subjects/fsaverage/label
doug
Vy Dinh wrote:
5.0
Dear Experts,
I ran the wm.mgz corrections and pial corrections using the command:
-autorecon2 –autorecon3 –subjid sub2
However, Freesurfer exited the program with the following message:
SUBJECTS_DIR/Users/subdir
FREESURFER_HOME Applications/freesurfer
Loading source label.
No such file or
...@rush.edu
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 12:26 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2
autorecon3
Does /Users/subdir
...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 12:51 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2
autorecon3
It does need to be there, but usually it creates it's own symbolic link
(so you should not need to copy it).
doug
Vy
,
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 1:10 PM
To: Vy Dinh
Cc
-4660
Email: vy_d...@rush.edu
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, October 13, 2011 3:13 PM
To: Allison Player
Cc: Douglas N Greve; Vy Dinh; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Automatic corrections log/diary
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a
brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It
would be great to view the edited voxels as anything but black and white (eg
dark blue and a
...@nmr.mgh.harvard.edu]
Sent: Thursday, October 13, 2011 2:10 PM
To: Douglas N Greve
Cc: Vy Dinh; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Automatic corrections log/diary and questions about
Tkmedit color options
I believe if you go to the View menu you can select Edited voxels which
will show what
Dear Experts,
I noticed that the inferior horn of the lateral ventricles are not included
within the pial surface while the posterior lateral ventricles are and wonder
how one should go about when making corrections for the pial surface. This was
observed in the subjects that I have worked
: Wednesday, September 28, 2011 4:16 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.gold...@gmail.com
Subject: Re: [Freesurfer] Inclusion of lateral ventricle in pial surface
Hi Vy,
no, it shouldn't. The pial surfaces are not trustworthy near the
hippocampus, and we don't use them
: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 16, 2011 7:38 AM
To: k...@nmr.mgh.harvard.edu
Cc: Jing Ming; s...@nmr.mgh.harvard.edu; Jennifer G Goldman; Vy Dinh; Freesurfer
Subject: Re: [Freesurfer] manual editting problem
p.s. you also have topological defects there, which you can
Dear Freesurfer experts,
Is there a way to save out ROIs for all the regions listed in the Freesurfer
LUT? I've found posts and tutorials for saving multiple labels from an
annotation file, saving an annotation file from multiple labels, and saving
rois via the GUI. However, I don't quite
38 matches
Mail list logo
