Hi all,
I used the freesurfer 5.0,there is a question in my reseach,may be not a
question!
When i view the results of analysis in the qdec window,why did i cannot change
the value of the Threshold,such as min(which had been seted with the value of
2) ,in the same way,the max is 5?If i want t
Dear List
Just to say that the below error turned out to be a problem with my
pathdef.m file.
Very best,
Lisa
On Mon, Apr 4, 2011 at 4:24 PM, Lisa Ronan wrote:
> Dear List
>
> I have recently come up agains the same problem as described below, namely
> the error when I compute lGI reads
>
>
Hi Saad,
Since there is no message indicating it stopped due to error, I would try
running it again as it most likely stopped due to the machine it was running
on. You can pick up where it left off by doing:
recon-all -make all -s mysubject
On Apr 7, 2011, at 12:25 AM, Saad Ramadan wrote:
> De
Hi Doug,
I ran fcseed-sess in Freesurfer 5.1, all the way through selxavg3-sess. How
can the results be visualized, given that no contrast was specified? In the
freesurfer wiki, it is said that "a contrast does not need to be made
because one is automatically created with an -taskreg". But without
how much memory do you have in that machine?
Bruce
On Thu, 7 Apr 2011, Saad
Ramadan wrote:
> Dear all,
>
>
> I ran (on an isotropic MPRAGE ):
>
> recon-all -subject mysubject -i
> ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all
>
> which ran for few hours and then exite
See the usage statement for 'mris_anatomical_stats' below -- just end
your command with the surface name (i.e., pial).
Also, you don't need the -t flag (lh.pial is not a thickness file, and
thickness is independent of whether stats are computed on the 'white'
vs. 'pial' surface).
usage: mris_ana
The contrast has the same name as the seed configuration. Or you can use
-call (for all contrasts) and it will find the one that you need.
doug
Y.V. Jiang wrote:
> Hi Doug,
>
> I ran fcseed-sess in Freesurfer 5.1, all the way through
> selxavg3-sess. How can the results be visualized, given tha
When you get p-values (sigs) out of FreeSurfer, the p-value is computed
assuming an unsigned test. This makes the p-value twice that of a signed
test (ie, it is less significant than the signed test). When you go to
correct for multiple comparisons and you specify a sign (positive in you
case),
Hi Bruce,
I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Fixing Bad Output From the Talairach Registration
FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix
in a file called talairach.xfm and is located in the /mri/transforms directory. Under so
For an odd number of slices- e.g. 45- would it just be
1,3,5,...,45,2,4,...,44 for the Siemens default?
On 2/9/11, Douglas N Greve wrote:
> For Siemens with an even number of slices, it is generally
> 2,4,6,..30,1,3,...29. This changes if there is an odd number of slices.
>
> doug
>
> Rita Loioti
yes
doug
Rita Loiotile wrote:
> For an odd number of slices- e.g. 45- would it just be
> 1,3,5,...,45,2,4,...,44 for the Siemens default?
>
> On 2/9/11, Douglas N Greve wrote:
>
>> For Siemens with an even number of slices, it is generally
>> 2,4,6,..30,1,3,...29. This changes if there is an o
Can you provide the full reference for the Kuperberg article?
On Fri, Mar 11, 2011 at 5:49 AM, Lena Palaniyappan <
lena.palaniyap...@nottingham.ac.uk> wrote:
> Hi Ri
>
> Have a look at Gina Kuperberg’s paper on cortical thickness in
> schizophrenia – she reports effect sizes
>
> Hope the rest is
Hello all,
I would like to take advantage of the gcut feature to remove dura that gets
included in many subjects in my dataset. I am using v5.0.0, but when i enter
the command from the wiki: recon-all -skullstrip -clean-bm -gcut -subjid
, i get an exit recon-all with errors, saying "ERROR: Fla
Hi Michael,
With 5.0, gcut is run by default I believe. If you look at the
recon-all.log for that subject and search for gcut, you should be able to
see if it ran.
Allison
On Thu, 7 Apr 2011, Dougherty, Michael wrote:
> Hello all,
> I would like to take advantage of the gcut feature to remove d
Hi Saad,
why do you think that the talairach was a problem? That wasn't what was
failing in your previous email
Bruce
On Thu, 7 Apr 2011, Saad Ramadan wrote:
> Hi Bruce,
>
> I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
>
> Fixing Bad Output From the Talairach Registr
Hi Ri,
it's on our wiki and should be pretty easy to find there. It's on
schizophrenia
Bruce
On Thu, 7 Apr
2011, Emily Rogalski wrote:
> Can you provide the full reference for the Kuperberg article?
>
> On Fri, Mar 11, 2011 at 5:49 AM, Lena Palaniyappan <
> lena.palaniyap...@nottingham.ac.uk>
Hi,
I'm trying to go through this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio
nSpm
I have already downloaded/unpacked the
buckner_data-tutorial-subjs.tar.gz, and also set up the correct
SUBJECTS_DIR as:
setenv TUTORIAL_DATA /Applications/freesurfer/subjects
That tutorial is out of date. Try using the multimodal below.
doug
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal
Palzes, Vanessa wrote:
> Hi,
>
> I'm trying to go through this tutorial:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio
> nSpm
>
> I have
Hello,
I did an FIR analysis and want to get the activation measure for specific ROI
at consequent time frames.
mkanalysis-sess -analysis context_FIR.rh -surface fsaverage rh -fwhm 5
-paradigm sca_wca.par -event-related -fir 4.4 17.6 -refeventdur 2.2 -mcextreg
-TR 2.2 -nconditions 2 -force
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