Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
ipsil
Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
ipsil
VP,
the recon-all stream produces ?h.ribbon.mgz and ribbon.mgz files which
are based on the surfaces, so that is your best option.
Nick
On Mon, 2013-03-11 at 15:28 -0400, Valtina Pouegue wrote:
> Hi Freesurfers,
>
>
> I would like to extract the whole pial surface of a brain volume. I
> alrea
Hi
What would be the best way to measure cortical surface either the white
surface area or pial surface? Is the total surface area calculated by
mris_anatomical the same pial surface?
When using QA tool which article should I cite?
Knut J
___
Freesurf
Hi Freesurfers,
I would like to extract the whole pial surface of a brain volume. I already
done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it
exist a way to get the whole pial surface without separation?
Thanks.
VP
___
I am thinking that that's possible. Same command with same type of
parameters executed successfully before the failure, and now previously
failed command is working. I will try it again...
Thanks for the input.
-Ronny
>
> Probably a network glitch? I'd try restarting it and seeing if the error
>
Probably a network glitch? I'd try restarting it and seeing if the error
persists.
On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
> It looks like this is the first *thresh.* label that caused the problem.
> The following command ran and executed properly just before the error
> messag
It looks like this is the first *thresh.* label that caused the problem.
The following command ran and executed properly just before the error
message on the log.
mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh
Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or
is BA3b.thresh the only one? If you remove the .thresh do you still get an
error?
Thanks,
a.y
On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
> Hello,
>
> I ran recon-all and left it running Friday afternoon/eve
Hello,
I ran recon-all and left it running Friday afternoon/evening. When I next
checked it this morning, the script had finished with errors. Looks like
there was a problem with the file:
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
/clus
Hi Christopher, I'm not sure I understand your question. What do you
mean by "simple measurements"?
doug
On 3/11/13 10:59 AM, Christopher wrote:
> Thanks Doug. I can know visualize the resected area using freeview.
>
> As the output of mri_vol2surf produces an overlay and not a surface,
> measu
Hi Jorge,
I see now:
/Y, Beta2, sided_pval/ - have the same number of columns
/fstats.pval/ and /fstats.sgn/ were not generated (or they are not in
the workspace) !
a.
Le 3/11 11:53, jorge luis a écrit :
Hi Alex
The cmd
/[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.s
Hi Alex
The cmd
[detvtx,sided_pval,pth] = lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0);
only takes a few seconds to finish. Please check if Y, Beta2,
fstats.pval,fstats.sgn, sided_pval
all have the same number of columns.
Best
-Jorge
>
> De: Al
Hi Laura,
If you're looking for another reference that has used this approach, you
could see our 2010 paper:
http://www.ncbi.nlm.nih.gov/pubmed/20118463
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Di
Hi Jorge,
I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2
Sinead,
In your freesurfer directory, is there an 'mni' directory? under that
directory is a 'bin' directory where nu_correct should be.
Nick
> Hi Nick,
>
> I had a look in the bin directory and there is a command called
> 'mri_nu_correct.mni'. Is this the command the script is trying to call?
Hi,
I have been working on a DBM based method to obtain longitudinal atrophy on
some brain data. To quantify ROI, i use aseg.mgz. Several papers talk about
Whole Brain, ventricular atrophy but do not actually define what
substructures they use? It will be great if somebody can help me get the
actu
Hi Nick,
I had a look in the bin directory and there is a command called
'mri_nu_correct.mni'. Is this the command the script is trying to call?
This is the only nu_correct command I could find. I specify v5.2 in the
script as there are other versions installed on the clusters.
Thanks again for y
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface,
measurements of area or/and intersection with other outputs from
mri_vol2surf are not possible using mris_* functions.
What is the best strategy to follow to b
Hi Charles, can you verify that brainmask.mgz exists for that subject?
What do you get if you run
stem2fname $SUBJECTS_DIR/$subject/mri/brainmask
doug
On 3/11/13 4:07 AM, Charles Malpas wrote:
Hi Doug,
I think I am having the same problem, but only when running on our Red
Hut cluster (Cen
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