What about:
freeview -v FA.nii.gz -v V1.nii.gz:vector=yes
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, March 17, 2015 11:57 AM
To: Freesu
Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi
[zribi.fa...@gmail.com]
Sent: Thursday, April 23, 2015 9:14 AM
To: freesurf
I have tools in R that can do #1, and network/graph theory analysis on top of
that. I plan to work on things like #2-3 but haven't yet (e.g. there is
possibly less consensus if region X is limbic vs. para-limbic, as opposed to
temporal vs. parietal).
I can send you something in a few days/a week
Doesn't that just mean your colleagues are editing the brains differently?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of amirhossein manzouri
[a.h.manzo...@gmail.com]
Sent: Tuesday, July 28, 2015 7:33 AM
To: Do
Just use either "system" or the exclamation mark and type the FSL commands
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S.
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
T
Ah, that's probably correct. I think it worked on my system because I source
the FSL conf file in my .bashrc
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sen
Andre, I haven't done any statistical comparison, but for my data (pediatric) I
found the DKT labels to be somewhat more accurate. The biggest differences were
in superior frontal and rostral middle frontal. Other differences I've seen are
anterior cingulate, cuneus, and fusiform. See Figure 4 i
I think it's a bit unclear what you're asking for. Have you followed the
tutorials on the wiki? Can you post your directory structure?
What I do on my system is keep studies separate from one another. Each study
directory has its own FS directory, and I keep the raw images separate. So
somethin
1. Yes, I would expect that
2. Because the pial surface is bigger. (Unless I'm misunderstanding the
question?)
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Gerrits, Niels
Sent: Thursday, August 27, 2015 10:36 AM
To: Freesurfer support list
Subje
>From your original mail: I agree with Dr. Kanwisher. When you ask if it is
>appropriate to "(visually) compare" list of regions, I would answer that it is
>absolutely not. A direct comparison is necessary. See e.g. Nieuwenhuis et al.,
>2011, Nature Neuroscience.
For your second, I would say t
Yes, they are 2 separate atlases. The references are on the FS wiki.
The "ctab" files are colortable files, so I believe the "25 100 40 0" are the
RGB + transparency/opacity
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard
You can read about it here:
http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/abstract
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of krista kelly
[krista.kell...@gmail.com]
Sent:
I only have anecdotal evidence based on 4 subjects, but I found that using the
FLAIR results in much better surface reconstruction than the multiecho. In my
experience (with kids age 12-16), the pial surface was underestimated when I
used the multiecho.
I don't want to speak for the Freesurfer team, but I am 99% certain that it is
Direct/Standard as you list them. There isn't any stepwise variable selection
going on.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] o
Dear Freesurfer users, (apologies for cross-post)
I am pleased to announce the release of an R package I created, called
"brainGraph", for performing graph theory analyses of brain MRI data. You can
use it for cortical thickness, volume, surface area, or LGI. It can also be
used for tractograph
The option should be:
--annot aparc.DKTatlas40
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman
[marmaduke.wood...@univ-amu.fr]
Sent: Wednesday, March 2, 2016 08:27
To: freesurfer@nmr.mgh.
Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:
recon-all -autorecon3 -s $SUBJECT -FLAIRpial
It has worked for me. (And worked very well! No edits necessary for the pial
surface!)
___
: Saturday, June 01, 2013 4:21 PM
To: Watson, Christopher
Cc: Freesurfer
Subject: Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2
Hello list,
we found the problem, symbolic links:
/home/glerma/ is the home of the app server where fs is installed.
/home/glerma/glerma/freesurfer/subjec
1) The right panel shows the aseg voxels. The surfaces are the same in L and R
panels.
2) What do the surrounding slices look like? It may be that the WM surface
"fills in" more as you go along.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-bo
I don't know, but I'm pretty sure the Freesurfer team will recommend you use
v5.3.0. There are emails saying as much.
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of clarissa yasuda
[clayas...@gmail
I've found that when using the Bash shell, putting multiple subjects in the
config file doesn't work. Maybe that's the issue here? Although, I simply never
bothered to look into it any more.
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer
This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
Indeed. It's actually really easy to set up, too.
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
yours look particularly good).
Is this a noisy dataset or something?
From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:32 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfe
Try this:
http://www.mail-archive.com/search?q=reinit&l=freesurfer%40nmr.mgh.harvard.edu
From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:51 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesu
You could probably load them in matlab and compare there.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Romano
[drom...@stanford.edu]
Sent: Thursday, September 05, 2013 8:01 PM
To: freesurfer@nmr.m
The problem here is that SZ*.nii presumably refers to a list of files due to
shell expansion. I don't know how recon-all handles that (e.g. if it will take
only the first file in the list, or all files), but that command probably won't
do what you want it to.
___
Thanks,
Chris
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 14, 2012 5:29 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE intensity variations
Hi Chris
Are you using prescan normalize? It helps a lot
Che
Hi Doug et al,
The 2nd question is something I've wondered about. Doesn't a Bonferroni
correction assume that the measures are independent?
If so, I think in the case of subcortical structures, it is incorrect to use
this method, as e.g. the putamen and pallidal volumes are not independent of
ed?
Thanks,
Chris
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 21, 2012 12:01 PM
To: Watson, Christopher
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC
Hi Chris,
bonferroni will be o
I've just taken to making the sym links myself after running trac-prep and
before running bedpostx. Then everything should run normally.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[
There were recently a few messages on the list regarding this.
What you should do is include "set reinit=1" in your config file, and then run
trac-all -priors -c $CONFIG
trac-all -path -c $CONFIG
Make sure you only include the pathway of interest in the config file;
otherwise, it will re-run the
I've had no problems with it.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Brain Apprentice
[bapprent...@gmail.com]
Sent: Tuesday, November 20, 2012 11:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Hi Bruce,
So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e.
is it worth squeezing another acquisition into a protocol?
Chris
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bru
Hi Bruce,
What if she created an FSGD file, and instead of just having "patients" and
"controls", she would have "patients1.5", "patients3", etc.? With over 400
subjects this should be feasible, i.e. the loss of d.f. is worth running the
combined analysis.
Chris
In this case, GLM stands for "General Linear Model", and not "Generalized
Linear Model" (although the former is a subset of the latter). See e.g.
http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models
From: freesurfer-bo
Are you sure your path isn't look for the older "trac-all" first? If you didn't
remove/overwrite it, that is.
Type "which trac-all" (without the quotes) and see if the correct one is shown.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@
I think certain filesystems don't support sym linking (e.g. FAT32). So that
might be it.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme
[katherine.da...@gmail.com]
Sent: Monday, December
Hi Nick,
So would you recommend I install Centos 6 on the new workstation?
In addition, I've run recon-all on a large study group (>100); I take it I'll
have to re-run all of them?
Thanks,
Chris
Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it
i
Hello Freesurfers,
Lately I've been scratching my head about image orientation problems. What I do
here is take the DICOM images and use mri_convert to convert them into SPM
Analyze format. The command I use is:
mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \
Hi, I'm interested in getting multiple nifti images for each time point,
similar to this old thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03317.html
i.e., for a scan of 5 minutes and TR = 3, I would like 100 separate nifti
images. This works fine when I set --out_type sp
the resolution.
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can
I was running a subject, and got this error:
recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010
make: ***
[/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1
The disk is not full, and permissions are in order. I've run several other
subjects with no problems
I've never had any problems with CentOS 4.x; I have had some with CentOS 5, but
that was only when trying to run tksurfer, and that's really only because I
didn't feel like playing around with it. I think it was an openGL issue, and
not specifically a Freesurfer issue.
_
You can also just run e.g. "nohup recon-all -autorecon-all -s doe_j &"
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Scott Burns
[sbu...@nmr.mgh.harvard.edu]
Sent: Tuesday, December 14, 2010 8:05 PM
To:
010 9:54 PM
To: Watson, Christopher
Cc: Nathan Dankner; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] running in the background?
You can make it work with nohup? In the past I've had trouble and my thinking
was that because recon-all starts many child processes, the currently
conti
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