Hi Bruce,
The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which
I downloaded from the McGills site (
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009). The
template has a range of values from 0-100. Then I combined the csf/wm/gm
masks (derived from the 2009c tem
We need more info. Please see
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 12/01/2015 04:43 PM, levi solomyak wrote:
> Dear experts,
>
> I've been attempting to generate a stats data table in qdec, but each
> time I get a "Index Error: list index is out of range" error. This is
> occurrin
Dear experts,
I've been attempting to generate a stats data table in qdec, but each time
I get a "Index Error: list index is out of range" error. This is occurring
when it is trying to parse the .stats file.
I've made sure that the files all line up exactly with the qdec table and
that SUBJECTS_
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Try adding --invertmtx to the mri_label2vol command. I don't think the
label2label command does anything, does it? Also, you might have better
alignment if you run recon-all on the mni152 brain, then use
mri_label2label to map the label from the individual into the 152 space
using the surface t
By default, FS uses unsigned (ie, two sided) tests. If you have an a
priori hypothesis about the sign, then you can use a signed test. When
you use a signed test, the p-value is that of the unsigned test divided
by two, ie, it is more significant. When you specify a sign for the MC
correction,
On 11/27/2015 08:42 PM, nellie wrote:
> Hi expert,
> Thank you for your reply. I had read the example tables, but I'm still
> not sure how to alter them into my analysis.Can you help me to check
> the matrix I designed and point out my mistakes? Thanks in advence.
> 3 classes ( A / B / C group)
Dear Freesurfer experts:
we would appreciate if anyone could advise on the sign
choice of Monte Carlo simulation, a
question we posted 2 days ago.
In examining QDEC results of a contrast of interest, we noticed
the results are mainly in cold color (blue), with only two small clusters in
warm
Dear FreeSurfer Users,
I sent an email to this maillist a couple of weeks ago asking help for the
error that I encountered after running 'recon-all -s ${Mysubject}
-hippocampal-subfields-T1' with freesurfer 6. The content of this email is
attached below. Since then, my colleague and I have been
Hi Ajay
can you explain your entire processing stream, including the details of
the acquisition? What sequence/coil/scanner was used? You could fix your
problem by looking at the defects on the inflated.nofix, overlaying
lh.defect_labels on it to see where they are, then figuring out what cause
Hi Bruce,
When looking at my top slices in brain ask I noticed that the gray/white
matter shows but the darker areas surrounding it are not present (this
usually goes to the edge of the brain). Could the large defects be a
result of having masked this out on the input file? I multiplied the
tem
Hi Falk
I don't think you need to rerun the qsphere. I'm pretty sure this is a bug
in mris_fix_topology for giant defects, but haven't finished tracking it
down yet
cheers
Bruce
On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
Hi Ajay,
you should
cp ?h.orig.nofix ?h.orig
cp ?h.inflated
Hi Ajay,
you should
cp ?h.orig.nofix ?h.orig
cp ?h.inflated.nofix ?h.inflated
with ? being l or r depending your hemisphere. After the fixing stage the
surfaces got damaged somehow, therefore you have to recreate it them. I’m not
entirely sure about the qsphere. Probably you have to run the -q
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