Hello,
I'm trying to run qdec on my own data and I'm trying to create fsaverage.
Following the wiki tutorial, I copied the command:
if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage
but I got the following error:
bash: syntax error near unexpected token `ln'
Can anyone help me in
Hi Louis,
thank you very much for your reply.
The problem with our data is that wm is too dark sometimes to use
control points (intensity is too inhomogenious in some parts). That's
why we would like to have the opportunity to just draw the wm where
needed. But for some reason it doesn't correct
Hi Tanja
why is the wm too dark? Can you tell us something about your data
(population, coil, scanner, etc...)?
cheers
Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova
wrote:
Hi Louis,
thank you very much for your reply.
The problem with our data is that wm is too dark sometimes to use
Hello Bruce. Thank you for your reply.
I am not sure why the wm is too dark. Our population is very stressed
(burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil
8ch, we use BRAVO sequence with 1x1x1mm voxels.
Compared to the dataset I worked with before (from 1.5T scanner), here
it may also be the 8 channel coil, which can make things hard, particularly
near the vertex. Dielectric effects are usually still pretty modest at 3T
although they are visible. I think control points would be your best bet.
cheers
Bruce
On Wed, 28 Mar 2012, Tetiana Dadakova
wrote:
Hello
Do you think 32ch coil would be better? We also have data with the
same scanner and same sequence, but 32ch coil. Although, visually,
32ch data is much more inhomogenious, especially in occipital part (it
is too bright). We were afraid that wm there would be hard to
distinguish from gm and that
in our experience the 12 and 32 channel coils are much easier to process
than the 8 channels, but it really depends on the coil geometry
Bruce
On Wed, 28
Mar 2012, Tetiana Dadakova wrote:
Do you think 32ch coil would be better? We also have data with the
same scanner and same sequence, but
Hi Doug,
These are Siemens DICOMs and I really don't know what happened
to these T1 files, we just got them in this format. Only one out of 32
datasets went wrong, so I consider it as an incident. The workaround
with dcm2nii worked fine. Nevertheless, if you are interested I can
upload the
Add --cwsig cwsig.mgh, then load cwsig.mgh as an overlay in tksurfer.
Set the threshold to 1.3 (cluster p .05).
doug
On 03/28/2012 07:48 AM, Tetiana Dadakova wrote:
Hello Doug,
I cancel my first question, I realized CWP values are in the same file.
Regarding second question, my cluster is
That might be scanner coordinates or it might be that they just took
into account the voxel size but used some other coordinate system. Can
you find out exactly what the coordinate system is? I really need that
information before I can give you an answer.
doug
On 03/27/2012 07:58 PM, Johnson
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography study
with TRACULA I can use my previous results from FSTutorial/Diffusion more
exactly my results after running dt_recon and registrations on the CVS space.
If not can you please advise me if for a DTI
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography
study with TRACULA I can use my previous results from
FSTutorial/Diffusion more exactly my results after running dt_recon and
registrations on the CVS space. If not can you please advise me if for
a DTI
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography
study
with TRACULA I can use my previous
Hi Anastasia,
Many thanks for your reply and help. I was wondering that instead to redo all
the preprocessing and registration steps s mentioned on FSTutorial/Running
Tracula:
* Eddy-current correction
* Intra-subject registration (diffusion data to T1)
*
Hi,
I would redo the processing for the Tracula processing as the FSL tools
require your data to be in a certain orientation and ours don't so you
might end up with some inconsistencies if you use the two packages
together.
Lilla
On Wed, 28 Mar 2012, Antonella Kis wrote:
Hi Anastasia,
Hello,
I am using FreeSurfer 5.1.0. When running
recon-all -label_v1 -s $SUBJECT
It could not find the rh.white and lh.white surfaces. Subsequently,
there was no data in the rh.v1.predict.label.
% tksurfer.bin: no data in label file
Hello freesurfers
I am using freesurfer for patients with various neural disease. I wonder
the the freesurfer atlas is applicable to them: dementia (with Lewy bodies,
DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some
studies already used freesurfer for some of the diseases in
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