Hi Surfers,
as of version 5.2, i'm getting an error using asegstats2table, depending on
how i sort the subjects:
andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECTS_DIR | sort -t _ -k
1 -nk 2) -t segstats.csv --skip -d comma
SUBJECTS_DIR : /mnt/raid/freesurfer/subjects
Parsing the .sta
Hi Andreas, fsaverage does not have stats files so should cause it to
crash. Are you saying that if you sort it in a certain way, you can get
it to run with fsaverage?
doug
On 04/24/2013 09:51 AM, Andreas Berger wrote:
> Hi Surfers,
>
> as of version 5.2, i'm getting an error using asegstats2t
Dear Freesurfers,
During the display of my data in tksurfer I smoothed my overlay with 1
smoothing step (Tools > Surface > Smooth Overlay... ).
All I could figure out was that this is done by sclv_smooth but what is exactly
happening mathematically in this case?
What does 1 smoothing step corres
For each step each vertex is averaged with its nearest neighbor. If you
use two steps, then this is done twice.
doug
On 04/24/2013 12:24 PM, Thomas Janssens wrote:
> Dear Freesurfers,
>
> During the display of my data in tksurfer I smoothed my overlay with 1
> smoothing step (Tools > Surface >
Hi Doug,
Sorry to follow this topic with a delay but we tried to model BOLD
signal undershoot with a gamma function and we failed. The problem is,
gamma function generates positive values and we can NOT use "inverse gamma
function" (or otherfunction similar to that) as a part of mkanalysis-sess
What do you mean the gamma function generates positive values? It will
create a regressor with a positive-going HRF. However, the regression
coefficient can be negative which would invert the shape. The reg coef
is fit to the data, so the data will tell you whether there is an
undershoot or no
dear FS experts
I have some PAR/REc format anatomical file from a Phillips scanner. I want to
convert the to nifti or MGZ format for freesurfer. how do I do this conversion
what program do I use?
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441
Hi all,
Is it possible to use the Tracula bedpostx data to run Probtrackx with
different seed points? For example:
1. Run all of Tracula on subject.
2. Extract seed masks from FS (eg seed superior temporal gurus to target
anterior insula).
3. Run Probtrackx with the dbedpost data and masks i
sorry, we don't have a way to convert par/rec files
doug
On 04/24/2013 03:50 PM, Jon Wieser wrote:
> dear FS experts
>
> I have some PAR/REc format anatomical file from a Phillips scanner. I want to
> convert the to nifti or MGZ format for freesurfer. how do I do this
> conversion
> what progr
You don't generate a negative coefficient. The sign and magnitude of the
coefficient is determined by the fitting procedure. It may be the case
that a positive coef fits the data better than a negative. You should
not change the gamma parameters.
doug
On 04/24/2013 04:06 PM, SHAHIN NASR wrote
This looks wrong:
W = TalXFM * Norig * inv(Torig);
If RAS = A.vox2ras1 * [i;j;k;1]; (Note: vox2ras = Norig), then
just
mni305 = TalXFM*A.vox2ras1 * [i;j;k;1]
One way to check is to display the MNI305 and ScannerRAS in the tkmedit
control window. Take the RAS from the control window, put it into
Hi MGH-ers,
>From where I sit (San Diego), http://surfer.nmr.mgh.harvard.edu/ seems to have
>been non-responsive at least since about 4 pm west-coast time. It's now 4:40
>pm.
http://nmr.mgh.harvard.edu is working fine.
Perhaps you are already on top of this, but in case not...
Thanks,
-- Gra
Hi Graham
yes, we have been the target of a denial-of-service attack and have taken
it offline for external users for a bit
Bruce
On Wed, 24 Apr 2013, Graham Wideman
wrote:
> Hi MGH-ers,
>
>> From where I sit (San Diego), http://surfer.nmr.mgh.harvard.edu/ seems to
>> have been non-responsive
Hi all,
I am looking for current recommendations for specs for a desktop Linux box for
running Freesurfer (and friends), both recon-all, and the interactive graphical
tools.
I have read the generic recommendations here:
http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
(also here as
Graham and other wiki users,
The wiki is still accessible if you use 'https' instead of 'http'.
Because wiki pages link to each other, you may run into links where you
need to repeat this change.
We're hoping the spambots that were slowing our wiki system will go away
if accesses continue to fai
Hello,I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered:mri_glmfit-sim \--glmdir GLMFIT/LH_1
Graham,
Hi, to answer each:
Intel vs AMD: no preference. also, CPU speed is not critical. Its
better to have at least 4GB, and budget 4GB per subject you want to
process simultaneously. Try to get a 'Sandy bridge' motherboard
architecture or whatever is newer. This allows better addressing o
I think Nick meant to say 400MB per subject, not 400GB per subject:)
On 4/24/13 8:42 PM, Nick Schmansky wrote:
> Graham,
>
> Hi, to answer each:
>
> Intel vs AMD: no preference. also, CPU speed is not critical. Its
> better to have at least 4GB, and budget 4GB per subject you want to
> proce
Hi Jeni, done pass that path to the csd, just the csd base. In your case
I think it would be 1GroupAvg-Cor-thickness-Mod-VAS
doug
On 4/24/13 8:47 PM, Jeni Chen wrote:
Hello,
I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I
specified the --no-sim option to avoid re-running the
You might use dcm2nii written by Chris Rorden
http://www.nitrc.org/projects/mricron
It is part of the MriCron package. For Windows, you can directly use the gui by
dragging the files on the GUI. For MAC or Linux use the command line.
Beste wishes,
Luke
Am 24.04.2013 um 21:56 schrieb "Douglas N
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