Hi,
I am trying to use mkanalysis-sess in version 5.1 with 5 external
regressors. I have prepared them as individual text files.
When I run mkanalysis-sess
-force
-notask
-a lot of other stuff
-taskreg seed1 1
-taskreg seed2 1
-taskreg seed3 1
-taskreg seed4 1
-taskreg seed5 1
-nuisreg global.wave
Thanks Derin. Can you send us a 4.5 case where the WM edits are
disappearing in 5.1?
doug
On 05/02/2012 04:42 PM, Derin J Cobia wrote:
> FWIW, in our experience this isn't always the case. When re-running edited
> and "cleared" subjects in 4.5.0 up to 5.1.0, we have had to return and
> re-edit
FWIW, in our experience this isn't always the case. When re-running edited and
"cleared" subjects in 4.5.0 up to 5.1.0, we have had to return and re-edit the
vast majority of these individuals order to obtain accurate surfaces. To be
specific, we are not finding control points or pial edits disa
Dear Michael,
Thank you for your answer! I will try it! but I have no knowledge about
Python. I have some Matlab code. Maybe I first wait Doug's answer. If his
answer is a little easier to understand for me, I will share here.
Thanks
Regards
Kathy
On Wed, May 2, 2012 at 6:32 PM, Michael Wa
Dear Doug,
Thank you for your reply soon. I would like to know further instructions
for doing this.
Thanks
Best wishes
Kathy
On Wed, May 2, 2012 at 5:59 PM, Douglas N Greve
wrote:
> Hi Kathy, there is not an easy way to do this. The closest thing you
> could do would be to create an annot
Hello Surfers,
Command: asegstats2table --skip --delimiter comma --common-segs
--stats=lh.BA.stats --meas volume --tablefile V5vo-BA-lh.csv
--subjectsfile=a.txt
I am trying to create a table of "lh.BA.stats" values where all
subject are listed in a.txt.
asegstats2table tries to work however ther
Hello,
The command
mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz
gives the following output:
mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from 0001_9746dc8a
Efrat,
Another point is whether it is worth the time to re-run your subjects
with 5.0.1. There is not much to be gained by doing so. Also, we're
hoping to have a 5.2 release in a month or so, so you might want to wait
anyway.
Nick
On Wed, 2012-05-02 at 11:55 -0400, Douglas N Greve wrote:
> It
Dear FreeSurfer experts,
How does one properly convert from surfaceRAS coords, as provided by
fs_read_surf.m, to talairach coords? I have tried using freesurfer_surf2tal.m
posted on the web by Darren Weber, supplying it with transform data from
transforms/talairach.xfm, but the values returned
Hi,
If you're somewhat handy with Python, you can use PySurfer for this.
See this example:
http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html
Best,
Michael
On Wed, May 2, 2012 at 7:51 AM, keepmoon wrote:
> Dear all,
>
> I search my question before I post it. I did find similar
Hi Tanja, we don't have a turn-key way to do this, but you can do it in
matlab using this function:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m,
something like:
cd glmdir
beta = MRIread('beta.mgh');
rvar = MRIread('rvar.mgh');
X = load('Xg.dat');
C = load('contr
Hi Kathy, there is not an easy way to do this. The closest thing you
could do would be to create an annotation with those 3 colors based on
the thresholded sig maps. Let me know if you want instructions to do this.
doug
On 05/02/2012 10:51 AM, keepmoon wrote:
> Dear all,
>
> I search my question
It's worth pointing out that your edits will be preserved, so it should
just be computer time.
On 05/02/2012 09:08 AM, Bruce Fischl wrote:
> Hi Efrat,
>
> no, we don't recommend this, otherwise you run the risk of increasing
> variance and introducing a bias.
>
> sorry
> Bruce
> On Wed, 2 May 201
After running mri_glmfit-sim to get the clusters, there should be a file
named something like cache.th20.abs.y.ocn.dat. This will have the
thickness for each subject averaged over each cluster (a column for each
cluster).
doug
On 05/02/2012 03:30 AM, ZhiLiangLong wrote:
> Hi all:
>After fin
Dear all,
I search my question before I post it. I did find similar questions, but
didn't find answer. I want to overlay two files with different colors. For
example, one is sig1.mgh from cortical thickness, the other is sig2.mgh
from area. I want to use tksurfer overlaying them with three colors:
Dear Ruopeng,
this happens with any surface, for example "bert" lh/rh.pial (that comes with
Freesurfer). I have attached a locally generated surface as well, but I would
guess that the problem is not the surface (files) but rather freeview itself
or an incompatibility maybe with the Centos 5 libra
Dear FS experts,
I try to look at correlation between thickness and performance. I run
mri_glmfit (using performance as covariate) and mri_glmfit-sim. After
this I get some significant clusters.
I would like to ask if I could get a correlation coefficient for these
clusters, or/and a regression pl
Would it be possible to send us the surface file that caused the crash?
So that we can replicate the problem?
Thanks,
Ruopeng
On 5/2/12 9:35 AM, Focke, Niels wrote:
> Dear experts,
>
> I have experienced some problems with freeview. When loading a surface (both
> for my locally generated surface
Dear experts,
I have experienced some problems with freeview. When loading a surface (both
for my locally generated surfaces as well as for "bert" surfaces) the program
exits (progress bar at approx. 10%) with this message:
MatrixMultiply: m2 is null!
The problem happens both for command line lo
Hi Efrat,
no, we don't recommend this, otherwise you run the risk of increasing
variance and introducing a bias.
sorry
Bruce
On Wed, 2 May 2012, Efrat Kliper wrote:
>
> Dear FreeSurfer expert,
>
>
> I am currently working on FreeSurfer Version 4.5.0 and already performed an
> analysis for a
Dear FreeSurfer expert,
I am currently working on FreeSurfer Version 4.5.0 and already performed an
analysis for approximately 200 subjects. Is there a way to change the
version that I am working on (4.5.0) to 5.0.1 without the need to run
recon-all again in the new version?
Thanks in advanced,
I don't think there's a difference - the thicknesses are the same in
fsaverage and individual space
cheers
Bruce
On Wed, 2 May 2012, ZhiLiangLong wrote:
Hi all:
After finishing group analysis, how can i obtain the thickness value of
each ROIs showing significant group-difference in fsaverag
Hi Mahinda,
For question 1, if you use the new mris_preproc, as described here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19821.html
then yes, you are safe in computing the areas for each vertex.
We have a recent paper that discuss current matters on pointwise area
stuff, a
Hi all:
After finishing group analysis, how can i obtain the thickness value of each
ROIs showing significant group-difference in fsaverage space? That is to say,
how i get the value of each ROIs which have been normalized to the fsaverage
template. The method suggested in tutorials
page(ht
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