Hello freesurfers,
I am trying to unpack a couple of recent subjects in Stable 4. I ran all
steps through recon-all without error. However, when I try to run the next
step, preproc-sess, it keeps failing.
This is the command I enter:
preproc-sess -s FB0011060AA -fwhm 5
It works for about 30 sec
Hi,
One of the volumes listed in the aseg.stats is
called "CSF". Its volume is too small to indicate
the total CSF volume of the brain. What is its
meaning?
If I would like to get the total CSF volume how
should I proceed?
Ed
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Hi Ed
you would need a T2 or PD scan for that. The CSF label isn't reliable and
only refers to bits of CSF here and there (not sure why the CMA included it
at all)
cheers
Bruce
On Wed, 22 Sep 2010, Ed Gronenschild wrote:
> Hi,
>
> One of the volumes listed in the aseg.stats is
> called "CSF".
Hi Tommi, that's going to be a problem because all the tools look at
the number of frames to determine how much data to read in (unlike voxel
size or direction cosines). I don't know of an easy way around it,
though I can think of some hard ones. How hard is it to fix the grappa
recon to wri
The 'fsledithd' utility (of FSL) can be used to edit the number of
frames (as well as a host of other fields) in a Nifti file.
cheers,
-MH
On Wed, 2010-09-22 at 09:02 -0400, Douglas Greve wrote:
> Hi Tommi, that's going to be a problem because all the tools look at
> the number of frames to d
Hello everybody
I'm wondering about how to perform an FDR correction using the glmfit on FS?,
I mean using command line if there is one;
And Could it be applied the same sentence to correct at cortex level and
clusters label, or need some special arguments on the command line for any of
them
Hello-
I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
but the old solution is not cutting it. When I try to load a table
in QDEC 1.4, I get the following error:
Loading
can you send me the file?
n.
On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
> Hello-
>
> I'm having a resurgence of an old problem
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
> but the old solution is not cutting it. When I try to load a table in QDEC
Hi:
What it means the "nframes" parameter ?... Which is the difference between a
001 mgz file that has "dimensions: 256 x 256 x 176" and another that has
"dimensions: 256 x 256 x 176 x 2" ?...
Sincerely,
Gonzalo Rojas Costa
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Of course, once I ask
for help I stumble immediately upon the solution. There appears to
be a limit to the number of columns that QDEC is willing to put up
with when reading in tables. If I create a table that only has the
few columns that I'm interested in (as o
the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176)
cheers
Bruce
On
Wed, 22 Sep 2010, Gonzalo Rojas Costa wrote:
> Hi:
>
> What it means the "nframes" parameter ?... Which is the difference between a
> 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has
Hi Bruce:
And how can I get only one frame ?... I don't know why the medical
technologist got the two frames...
Sincerely,
Gonzalo Rojas Costa
Bruce Fischl escribió:
> the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176)
>
> cheers
> Bruce
> On
> Wed, 22 Sep 2010, Gonza
there shouldn't be a limit on the number of columns it will read. the
thing to be careful about is the name of a column. sometimes when
importing a spreadsheet, a column name will consist of two words (thus
messing-up the detected number of columns), or it will have a minus "-"
char in the name,
you can use mri_convert --frame 0 to get the 1st frame.
doug
Gonzalo Rojas Costa wrote:
> Hi Bruce:
>
> And how can I get only one frame ?... I don't know why the medical
> technologist got the two frames...
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
> Bruce Fischl escribió:
>
>> the 2nd
There is not a command-line program to do this. You can do it inside of
tksurfer. You can also load your significance maps into matlab, convert
to p-value, then use fast_fdrthresh.m
doug
Gabriel Go.Es. wrote:
>
> Hello everybody
> I'm wondering about how to perform an FDR correction using the
Dear Freesurfers!
I am a new user of freesurfer and I intend to install it on a HPC system.
There are two different systems available (see end of message). Could you
please give me a hint which one is best suited wrt hardware and software.
In order to use these systems one also has to state some
Hi Mo,
It means that you have an old version of fsaverage in your SUBJECTS_DIR
or linked to your SUBJECTS_DIR. Try using the one in
$FREESURFER_HOME/subjects/fsaverage
doug
Zeidan, Mohamed A. wrote:
> I got the following error when running isxconcat-sess:
>
> ERROR: cannot find
> /space/gro
the second option is best because it uses the x86 processor (amd
opteron), which is our common distribution. the first option uses the
Itanium processor which we dont actively support because we no longer
have access to a build machine.
the recon-all stream is not parallelized so you wouldnt bene
More news on the free brain atlas app for IPhone using FreeSurfer aseg.
Today we have another major upgrade:
- Pinch and Zoom
- Many papers for Reading
- Improved documentation of FreeSurfer
http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8
Suggestions for the upcoming version are
I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5)
through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't
look like a legacy analysis (see below).
[jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001
ERROR: you have specified -legacy,
yes, the -legacy flag was only necessary for the v3.0 to v4.0
transition. v4.0 data should be fully compatible with reprocessing in
v5.
n.
On Wed, 2010-09-22 at 17:31 -0500, Juranek, Jenifer wrote:
> I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5)
> through FSv5.0.0. Af
http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8
The download link for United States
-- via iPhone iOS4
Em 22/09/2010, às 20:50, Nick Schmansky escreveu:
>
> On Wed, 2010-09-22 at 19:17 -0300, Pedro Paulo de Magalhães Oliveira
> Junior wrote:
>> More news on the free brain atlas
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