Hi Bruce,
Actually I did my comparison just like that, but I just double checked
the face lists and they match. Thanks!
-Tuomas
On 09/02/12 16:38, Bruce Fischl wrote:
> Hi Tuomas
>
> the patch face list will be a subset of the full one. Note that because
> faces can be excluded from the patch
Dear all,
I'm not familiar with Freesurfer and I have a very naive question...
I'm reading with Matlab the .thickness files of a few subjects and I see
that there are some nearly zero / zero values.. how do I interpret them?
Maybe they correspond to regions which are not considered as cortex?
Had I
Hello,
I am using a DELL precision T3500 on Mandriva 2008
my SUBJECTS_DIR is :
/neurospin/grip/protocols/MRI/childrenNS5_7y_Monzalvo_2012/Subject/
(from the "neurospin/grip" network in my lab).
I am using the 5.1 version of freesurfer.
An the command line I ran was
recon-all -s ab080228 -a
Hi everyone,
I'm using optseq2 to optimize a fmri design.
Whenever I try to add the --tnullmin parameter I end up with either a
segmentation fault or a glibc error (see examples).
May someone explain me what is going wrong?
Thanks!
Regards,
Jacob
Info: optseq2 2.14 linux 64-bit and 32-bit
Examp
Hi everyone,
I'm using optseq2 to optimize a fmri design.
Whenever I try to add the --tnullmin parameter I end up with either a
segmentation fault or a glibc error (see examples).
May someone explain me what is going wrong?
Thanks!
Regards,
Jacob
Info: optseq2 2.14 linux 64-bit and 32-bit
Exampl
Hi Moran
1. Use the architectonic labels in the label dir (e.g. lh.BA4a.label,
lh.BA4p.label, etc...)
2. Mean curvature is in 1/mm
3. You can always load a curv map as an overlay (file menu) then use
different colormaps.
4. See 3 and change the overlay thresholds
what parameters do you me
glad to hear it
Bruce
On Fri, 10 Feb 2012, Tuomas Tolvanen wrote:
> Hi Bruce,
>
> Actually I did my comparison just like that, but I just double checked the
> face lists and they match. Thanks!
>
> -Tuomas
>
>
>
> On 09/02/12 16:38, Bruce Fischl wrote:
>> Hi Tuomas
>>
>> the patch face list will
Hi Gabriele
there are non-cortical regions in the surfaces to make them closed, and
these should have thicknesses that are identically zero in the interior
and probably very small right at the edge. We generate a label named
?h.cortex.label for each subject that represents the valid cortical pa
Hi Priti,
Thanks for your help. I took another look at the original diffusion and
anatomical images. The anatomical looks OK, but in the diffusion image a
posterior region of the brain appears cutoff and when I view the image in
freeview there is a green box in the lower left hand corner that I've
Hi Kiely - If part of the brain is cut off in dwi_orig.nii.gz, it means it
was cut off in your original dicom. If there's actualy part of the brain
missing in all the volumes in your diffusion series, you may not be able
to reconstruct tracts that go through that part.
a.y
On Fri, 10 Feb 20
Dear Experts,
Is it possible to link the four panel display so that as we are scrolling
through each slice in one view, the other three views will automatically
scroll to the next slice (without having the user click the cursor on a new
point)? This was possible in SPM Display tool, so I wonder if
Hi Daniel, can you send me the analysis.info and Xtmp.mat files?
doug
Daniel Cole wrote:
>
> Hello Freesurfers,
>
> I think my last email failed to send so here it is again -
>
>
> I'm running into problems using fs-fast for a polar only, retinotopic
> analysis.
>
>
> The error message I get is:
I don't think this is possible.
Vy Dinh wrote:
> Dear Experts,
>
> Is it possible to link the four panel display so that as we are
> scrolling through each slice in one view, the other three views will
> automatically scroll to the next slice (without having the user click
> the cursor on a new
I think freeview does this though, doesn't it?
On Fri, 10 Feb 2012, Vy Dinh
wrote:
> Dear Experts,
>
> Is it possible to link the four panel display so that as we are scrolling
> through each slice in
> one view, the other three views will automatically scroll to the next slice
> (without havi
Hello,
I had posted this question earlier but no one picked it up so I am trying
again. Briefly, I have been having difficulties with the very first step of
the recon-all pipeline, namely, in conversion of my dicom datasets to
freesurfer's mgz format. The error message (attached below) suggests tha
Hi Hemant
sorry for missing your previous post. I'm not sure what to tell you though,
if the direction cosines are nans that's going to be trouble. You could
still visualize your data in a slice viewer, but you may never be able to
tell left from right. Where did you get the dicoms? Are they r
Hi Bruce,
Thanks very much for your prompt reply. I am puzzled that freesurfer
doesn't get the direction cosines. Which fields is it looking for in the
dicom metadata ? When I load the slices in Matlab, I can see
ImagePositionPatient and ImageOrientationPatient and SliceLocation and they
all seem r
hmmm, I'll wait for Doug to comment as he knows far more about the dicom
stuff than I do
Bruce
On Fri, 10 Feb 2012, Hemant Bokil wrote:
Hi Bruce,
Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't
get the direction cosines. Which fields is it looking for in the dicom
Hi Doug and FreeSurferers,
I came across this email chain and am having a similar problem. I am working on
an interaction between a categorical and continuous variable, covarying for a
categorical variable. (E.g. the interaction between group membership and age,
covarying for gender). I know th
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