Hi Amelia - I guess the questions are what would be the end ROIs for a
connectivity matrix derived from tracula, and what would be defined as
connectivity strength. What's the goal of this analysis?
a.y
On Fri, 22 May 2015, Versace, Amelia wrote:
Dear Anastasia,
Is there a way to get
Hi Gabriella,
I'm not an expert in freesurfer. I've worked with freesurfer for 5 years
now. When we started I had the same problem when including ICV in the qdec
table and running it as a nuisance variable. I'm assuming you have ICV in
mm^3. Try converting it to cm^3 or dcm^3 in your qdec table.
Dear Anastasia,
Is there a way to get connectivity matrices using the outputs of tracula?
Thanks a lot, Amelia
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The information in
I got it.
Thanks a lot
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 3:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Standard deviation
Hello,
So recon-all seems to be running on my Mac fine, with this same data. But
it does not run on my institution's Minerva linux server.
It did most of volumetric processing steps, but failed on surface
processing steps, and then all of the rest.
I have checked that environment variables are
Hi list,
I'm configuring mkanalysis-sess to configure an analysis for FC data by
FS-FAST. I do not understand how I can perform mni305 volume-based analysis.
How can I configure an analysis for mni305? Specifically, which is the paradigm
file in
-taskreg? How is the command for group level
yes, but the ones in V6 (which someday will make it out) are more
accurate. You can get a beta and try them out if you want.
cheers
Bruce
On Fri, 22 May
2015, Hassan bakhshi wrote:
Hi,
I am using freesurfer v5.3, can I have hippocamp subfields in this version??
Kind regards
HI FS experts,
I haven't heard back and am still wrestling with these questions. Any takers?
I'd really appreciate any thoughts at all if possible.
Thanks,
Gabriella
From: Hirsch, Gabriella
Sent: Wednesday, May 20, 2015 3:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: ICV correction for
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see
the command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA. Kindly how
TRACULA is calculating the SNR
Hi Michelle - If you want to regenerate the stats with a different
threshold for a specific tract, you can run the dmri_pathstats command and
use the --pthr option with something other than the default 0.2.
You can search your trac-all.log file to see the dmri_pathstats command
line that's
Hi Jesse
the thickness files are scalar fields over the surface, not surfaces
themselves. Load it as an overlay, not as a surface
cheers
Bruce
On Fri, 22 May 2015, Jesse Bledsoe wrote:
Hi everyone,
I searched the wiki and old posts but couldn't find a solution to this
issue.
I had no
Hi Scott - The gradient table produced by dcm2nii is formatted in 3 rows,
rather than 3 columns. If you want to use gradient tables formatted in
rows, you have to download the tracula update described here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
a.y
On Tue, 7 Apr
Hi
I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I
start mri_convert on ubuntu 14.04.4 I get this results.
knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME=
/usr/local/freesurfer60
knutjb@dmed4960:/usr/local/freesurfer60$ source
That particular developmental build is compiled with optimization flags
for machines containing Intels new Haswell processor and wont run on
platforms without it. Although that build is available via our dev
download page, it remains an unsupported build that exists primarily for
internal
Hi Katherine - Is your gradient table in 3-row format by any chance? This
only works with the tracula update that was posted after the freesurfer
5.3 release. If you reinstalled freesurfer (as you mentioned earlier) you
might have overwritten the update, in which case the row-formatted
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}'
dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be
Hi Lucas - Only if you had DICOM files, you'd be able to specify one of
the dicom files and it would find the rest if they're all in the same
directory.
But if you have any other format (NIfTI in your case), then all the
volumes from a subject's diffusion scan should in one file. I you have
Hi everyone,
I searched the wiki and old posts but couldn't find a solution to this
issue.
I had no problems with the full recon-all script though got hung up trying
to load surfaces in tksurfer. The surface files are there but the buttons
in tksurfer aren't bright so I tried to load them
Hi Michelle - To bypass eddy-current correction, you set doeddy = 0 in
your config file. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
To skip the tensor fit step altogether you use the -notensor option in
trac-all. See:
Hi zeke
Do you know if version that support non Haswell cpu will be available?
Knut Jørgen
On 05/22/2015 06:06 PM, Z K wrote:
That particular developmental build is compiled with optimization flags
for machines containing Intels new Haswell processor and wont run on
platforms without it.
Were still in discussions about that. If the centos7 build (non-Haswell)
does not provide any significant reliability or performance advantages
than the centos6 build than we may just continue with the centos6 build.
-Zeke
On 05/22/2015 02:54 PM, Knut J Bjuland wrote:
Hi zeke
Do you know if
what is a .cshr?
do i just type the long command at the command line? sorry if this is a dumb
question
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]
Hi Celine - In an individual pathstats.byvoxel.txt file, the (x,y,z)
coordinates are given for every point along the tract, so you can
calculate the distance between consecutive points.
If you use trac-all -stat to put stats together across multiple
subjects, then in the *.log files generated
Hi Lars - A path with fewer control points will generally be smoother. So
if the tract is pretty much a straight line, you might get a noisier
result if you increase the number of control points. But if the tract is
more convoluted than a straight line, then you need more control points to
There's no perfect way to estimate SNR unfortunately. For example, using
the background outside the brain would mean that you'd be using locations
outside the head coil, and the noise there is not going to be
representative of the noise inside the head coil.
On Fri, 22 May 2015, Alshikho,
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing the
mean intensity for an ROI by the standard deviation for the same ROI so why the
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my
The Department of Psychiatry at the University of California, San Diego is
pleased to invite applications for a postdoctoral research scholar position in
neuroimaging and behavior genetics under the direction of Drs. William Kremen
(Psychiatry) and Anders Dale (Radiology and Neuroscience). The
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print
$1/$2}' dwi_snr.txt
the flag -m is the mean intensity and the flag -s is the standard deviation for
the intensity
Here we are using the same mask White-Matter++.flt.nii.gz so the output is
Standard deviation is the variation around the mean. The more the noise,
the more the variation.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}'
dwi_snr.txt
the flag -m is the mean
Hi Alan - If you were analyzing a volume (or area or length) measure, it'd
make sense to include something like ICV. If you're analyzing an
anisotropy or diffusivity measure, you wouldn't expect those to be
affected my how big the head is.
Best,
a.y
On Sat, 25 Apr 2015, Alan Francis wrote:
Hi Efrat - I'm guessing that you specified in your config file that you
want to perform B0 field inhomogeneity correction (set dob0 = 1) but
perhaps did not specify the B0 field map magnitude files correctly (set
b0mlist = ...) I'm guessing this because of this line in your log:
mri_convert /
Hi Xiaofu - The bedpostx program is not configured to run on any type of
cluster with any type of queueing software. It was originally written to
be run on an SGE cluster with specific queue names. The bedpostx_mgh is a
modified version that also works on our PBS cluster. Making it work on
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