I am sorry I meant gray matter comparison. Is QDEC GUI toolbox ready at this
point to do a vertex-wise gray matter comparison?
Sent from my iPhone
On Jan 28, 2014, at 5:33 PM, Douglas N Greve wrote:
>
>
> Do you mean having a different model at each vertex (like the --pvr
> option for mri_
Dear Doug
Thank you for the prompt reply.I want to make sure: If there is no group*age
interaction, is it safe to report the result of group differences using DODS (1
-1 0 0 )?Or is it more appropriate (or mandatory) to further use DOSS to look
for group differences (1 -1 0)?The reason why I a
Do you mean having a different model at each vertex (like the --pvr
option for mri_glmfit)? No, sorry
doug
On 01/28/2014 07:21 PM, Manish Dalwani wrote:
> Dear Freesurfer developers,
>
> Is QDEC GUI toolbox ready at this point to do a vertex-wise GM comparison?
>
> Regards
> Manish Dalwani
> In
Dear Freesurfer developers,
Is QDEC GUI toolbox ready at this point to do a vertex-wise GM comparison?
Regards
Manish Dalwani
Instructor
Dept. of Psychiatry
Univ. of Co
Sent from my iPhon
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h
All vertices in the cluster will have this value. It can be found in the
"summary" file in each contrast. It is the final clusterwise p-value,
ie, the probability of seeing a cluster of the given size by random chance.
doug
On 01/28/2014 05:07 PM, Natasha Haris wrote:
> Where does it appear
You can do it in QDEC by going running QDEC, then loading the surface,
curvature, and overlay files (they are in the output folder (default
"Untitled")). Load the "sig.mgh" file for the overlay. This can also be
done in tksurfer.
doug
On 01/24/2014 11:11 AM, Estephan Moana wrote:
> Dear Frees
QDEC computes it
On 01/28/2014 04:52 PM, Natasha Haris wrote:
> And does the monte carlo precomputed simulation data in the QDEC GUI
> compute this final p-value? Or do I need to use any commands namely
> mri_glmfit?
>
>
> On Tue, Jan 28, 2014 at 1:38 PM, Douglas N Greve
> mailto:gr...@nmr.mg
The cluster-forming threshold is needed to define what the clusters are.
Once you have a cluster forming threshold, you get clusters with a
certain size. Given the size, the FWHM, the cluster forming threshold,
and the search space, a p-value for the cluster is computed.
On 01/28/2014 03:58 PM
So sorry for all the beginner questions. One more.
Then what is the point of running the Monte Carlo simulation with a
cluster-forming threshold of p<0.01 or any other threshold for that matter if I
already know what the clusterwise threshold min should be?
Natasha
> On Jan 28, 2014, at 1
Yes
On 01/28/2014 03:35 PM, Natasha Haris wrote:
> So then how does one determine what should go into the Threshold min
> box? (If it's usually p<0.05 should the clusterwise corrected
> Threshold min be 1.3?)
>
> Natasha
>
>
> On Tue, Jan 28, 2014 at 12:30 PM, Douglas N Greve
> mailto:gr...@n
So then how does one determine what should go into the Threshold min box?
(If it's usually p<0.05 should the clusterwise corrected Threshold min be
1.3?)
Natasha
On Tue, Jan 28, 2014 at 12:30 PM, Douglas N Greve wrote:
>
> On 01/28/2014 03:26 PM, Natasha Haris wrote:
>
>> Oops sorry!
>>
>> I g
On 01/28/2014 03:26 PM, Natasha Haris wrote:
> Oops sorry!
>
> I guess my question then is, after running the monte carlo simulation
> with this cluster-forming threshold (p<0.01), is there a specific
> corrected (clusterwise) threshold I can/am supposed to place in the
> Threshold min box? Or
Oops sorry!
I guess my question then is, after running the monte carlo simulation with
this cluster-forming threshold (p<0.01), is there a specific corrected
(clusterwise) threshold I can/am supposed to place in the Threshold min
box? Or are these two not related in any way.
Natasha
On Tue, Jan
Hi Natasha, please remember to post to the list! When you say a
different set of blobs, do you mean that none of the original blobs are
there? Or do some of the blobs just disappear? Note that the threshold
you use in the simulation is not related to the "Threshold Min". In this
case, the Thre
Thanks for your help.
On Tue, Jan 28, 2014 at 11:53 AM, Lilla Zollei
wrote:
>
> I would say that for 5-8 the atlas would probably work. Below 5 I would be
> skeptical. There is no alternate atlas at the moment, but we are working on
> it.
>
> -Lilla
>
>
> On Tue, 28 Jan 2014, Mher Alaverdyan wro
Hi Rotem,
Check out the -dti flag in freeview, pass it a vector and FA volume. You
can display the colormap as vectors as well once everything is loaded up.
Example command:
freeview -dti V1.nii.gz FA.nii.gz
-Louis
On Mon, 27 Jan 2014, Rotem Saar wrote:
> Hi,
>
> We followed the instructions
I would say that for 5-8 the atlas would probably work. Below 5 I would be
skeptical. There is no alternate atlas at the moment, but we are working
on it.
-Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
> They are 2 - 8 years old.
>
>
> On Tue, Jan 28, 2014 at 11:46 AM, Lilla Zollei
>
They are 2 - 8 years old.
On Tue, Jan 28, 2014 at 11:46 AM, Lilla Zollei
wrote:
>
> Hi,
>
> What is the age range of your subjects?
>
> Lilla
>
>
> On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
>
> Hi all,
>> I just wanted to know if it is acceptable to use the Destrieux atlas in
>> FS for parcel
Hi,
What is the age range of your subjects?
Lilla
On Tue, 28 Jan 2014, Mher Alaverdyan wrote:
> Hi all,
> I just wanted to know if it is acceptable to use the Destrieux atlas in FS
> for parcellation of brain images of pre-adolescents. If not this atlas, then
> which would be a recommended a
Yes, when looking at the corrected images, the Threshold Min because the
clusterwise threshold. So if you want to see only clusters that have a
clusterwise p<.05, set that threshold to 1.3
doug
On 01/28/2014 02:24 PM, Natasha Haris wrote:
> The clusterwise simulation runs with a p<0.05 thr
Hi all,
I just wanted to know if it is acceptable to use the Destrieux atlas in FS for
parcellation of brain images of pre-adolescents. If not this atlas, then which
would be a recommended atlas to use for this population.
Thanks
Can you send the terminal output that starts with mris_preproc?
On 01/28/2014 02:01 PM, Wanda Truong wrote:
> Hi everyone,
>
> I get this error when running surface area analysis in QDEC:
>
> Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y
> /Users/vinagoghari/Documents/Wanda
you don't really need save and goto in freeview since you can load the
surfaces and the volumes together. The easiest thing to do is to copy the
vertex number from where you click on the inflated (in inflated part of the
info panel), then paste that into the white surface info panel so that the
Hi everyone,
I get this error when running surface area analysis in QDEC:
Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods
--glmdir
Dear Zeke,
Thanks for stepping in!
$ LIBGL_DEBUG=verbose tkmedit bert orig.mgz
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
libGL error: failed to load driver: swrast
Reading /usr/local/freesurfer/t
Hi!
This has popped up on the list several times already, but I was wondering
whether someone has figured out how to bring the F99 surface atlas from
Caret into Freesurfer (not Freesurfer to Caret)?
Thanks, Caspar
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sorry, try now
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
>
> Hi Freesurfer team,
>
> I noticed that the xhemireg file is missing from:
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
>
> I’m assuming the xhemireg for v5.3.0 (found in v5.3.0’s
> $FS_HOME/bin/xhemi
On 1/28/14 7:03 AM, KimMJ wrote:
Dear Doug and experts
My question is about the choice of DODS or DOSS.
I want to compare cortical thickness between 2 groups (disease group
and control group), while controlling for the effect of age (nuisance
covariate).
I've already read through the mailing
If you previously had XQuartz installed, then upgraded to Mavericks, it
may have written over the relevant files. Please install Xquartz and
give it another try. Thanks.
-Zeke
On 01/24/2014 05:33 PM, Dusan Hirjak wrote:
> Hi Zeke,
>
> sorry, I did it again and got the following output:
>
> /opt
Hi Freesurfer team,
I noticed that the xhemireg file is missing from:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
I'm assuming the xhemireg for v5.3.0 (found in v5.3.0's
$FS_HOME/bin/xhemireg) is identical and I can use that with v5.1.0?
Thanks,
Adam
___
Markus,
I have never seen those errors before. But a little googling suggested
perhaps running the program as follows:
~$ LIBGL_DEBUG=verbose ./tkmedit bert orig.mgz
Im a little at a lose at what else to try because we have freesurfer
installed on pretty much stock Ubuntu platforms and it runs
changing amygdala to hippocampus shouldn't change the surfaces at all. If
you upload the subject I'll take a look
On Tue, 28 Jan 2014, Thomas Fink wrote:
Yes, all we did in this case was change amygdala to hippocampus and in other
cases white matter to hippocampus or vice versa.
Thomas Fink D
Yes, all we did in this case was change amygdala to hippocampus and in
other cases white matter to hippocampus or vice versa.
Thomas Fink
Doktorand & wiss. Mitarb.
Lehrstuhl für Neuropsychologie
Mail: thomas.f...@psy.lmu.de
Phone: +49(0)89/2180-3123
On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl
Hello, FreeSurfer community,
I'm trying to run TRACULA sequentially.
After running, "trac-all -prior -s -i -c
"
that shows an error "Segmentation fault (core dumped)" in my server.
(Other options, "-corr, -qa, -intra, -inter, -masks, -tensor", were have
done without error)
Server was configure
The Hospital of the University of Munich, Germany, is one of the largest and
most competitive university hospitals in Germany and Europe. 45 specialized
hospitals, departments and institutions harboring excellent research and
education provide patient care at the highest medical level with appro
Dear Doug and experts
My question is about the choice of DODS or DOSS.I want to compare cortical
thickness between 2 groups (disease group and control group), while controlling
for the effect of age (nuisance covariate).I've already read through the
mailing list about the issue of DODS and DOSS
Dear experts,
We have a pool of 490 subjects and will work on a linux grid for the recon.
For this analysis we are only interested in subcortical areas.
Question:
Is it possible to run only the subcortical segmentation (and leave out the
cortical segmentation)?
(Is it possible to run the -subcort
Dear all,
For the error
> freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
> open shared object file: No such file or directory
sudo apt-get install libjpeg62
did the trick. Freeview is running fine
For the error
*libGL error: failed to load driver: swrast*
*libGL err
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