I think the right way is to weight by the area, but for those 3 I bet it
makes almost no difference.
doug
On 8/20/14 5:34 AM, elisa veronese wrote:
Dear FreeSurfers,
suppose I should estimate the mean cortical thickness on a number N of
ROIs (for instance, the left inferior temporal, the
Dear TRACULA experts
Hello.
I am running TRACULA, but it exited an error very early in pre-processing.
My data is not a format in DICOM but .nii, does this cause the error?
I set the dcmlist to .nii file (in attachment).
Could anyone help me?
This is the error log and I attached the configuratio
how did you create the head surface?
On 08/21/2014 01:42 PM, Meryem Ayse Yucel wrote:
> Hi freesurfer community,
>
> I am trying to get faces and vertices of the head surface mesh in Matlab.
> freesurfer_read_surf works perfectly when I extract faces and vertices for
> the pial surface (from lh.pi
It looks like your fsgd file may have been created on a windows
computer. Is that possible? Try reformatting it in linux or mac.
doug
On 08/20/2014 12:58 PM, Robby De Pauw wrote:
>
>
>
>
>
>
>
> Hi there FreeSurfer
>
> When trying the GLM-analysis I keep getting the following error. Could
> yo
Create a label of the cluster, then run
mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1
--avgwf cluster.dat
where y.mgh is the file created by qdec in the qdec output folder and
make sure to use the full path to the label. The output will be
cluster.dat and it will hav
One thing you can try is to run this:
cat whiplash.fsgd | sed 's/\r/\n/g' > new.whiplash.fsgd
doug
On 08/21/2014 01:30 PM, Douglas N Greve wrote:
> It looks like your fsgd file may have been created on a windows
> computer. Is that possible? Try reformatting it in linux or mac.
>
> doug
>
> On
Hi freesurfer community,
I am trying to get faces and vertices of the head surface mesh in Matlab.
freesurfer_read_surf works perfectly when I extract faces and vertices for
the pial surface (from lh.pial), but I get an "unknown magic number in
surface file" error when I use the same function for
Hi Nicholas
I'll cc Matti Hamalainen who should be able to help you, as he does this
kind of thing routinely within his MNE package.
cheers
Bruce
On Wed, 20 Aug 2014, Nicholas Heugel wrote:
I am running analysis where I am taking fMRI data using Freesurfer to
project it onto the cortical su
Dear FreeSurfer,When I try to use TRACULA I keep getting the following error:mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecsmv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/d
Hi Mads
what does it look like if you move off the mideline? Or check a coronal
view? Sagittal views of the midline are notoriously bad for judging skull
stripping accuracy
cheers
Bruce
On Tue, 19 Aug 2014, Mads Jensen wrote:
> Dear list,
>
> I have problem with the brainmask from a subject wh
Hi Mohammed
these are dark regions, usually in inferior pallidum/putamen. There
intensity is different enough from gray matter that having it be a separate
class helps us label them more accurately. They could also be lacunae and
not vessels.
cheers
Bruce
On Tue, 19 Aug 2014, Mohammed Gory
Hi Alejandra
you can do:
mri_convert -rt nearest -rl rawavg.mgz aseg.mgz aseg.rawavg.mgz
this will put it back in the scanner coordinates. Note that all of our
results are in subject space (not e.g. MNI), but they are in slightly
different ("conformed") voxel coords.
cheers
Bruce
p.s. -rt ne
Hi Jidan,
Can you upload one of these subjects so I can take a look?
You can use these options to upload data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Best,
Lee
From: freesurfer-b
Thank you Doug for this reply !
Best,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2014-08-19 16:55 GMT+02:00 Douglas Greve :
>
> By using --sfmt curv and --tfmt curv you are saying th
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