Dear Freesurfers,
I just have some quick questions regarding qdec:
1. How many covariates does the latest version of qdec allow you to
select? I am using FS version 4.3.0 and I cannot select more than 2
continuous variables. I am just wondering if a newer version allows you
to selec
Subject: POSTDOCTORAL POSITION - structure & function of fronto-cerebellar
circuits in neurodevelopmental disorders
Applications are invited for an immediate postdoctoral opening in the
Department of Psychology at the University of Houston, Houston TX. The position
is full-time for 1 year, wi
Thanks again. You have been very helpful
On Wed, Jul 8, 2009 at 4:11 PM, Bruce Fischl wrote:
> you don't have to - we will. You just draw it on the surface and tksurfer
> will figure out the volume coords and store them in the label file when you
> save it. You can then load it in tkmedit to see
you don't have to - we will. You just draw it on the surface and tksurfer
will figure out the volume coords and store them in the label file when
you save it. You can then load it in tkmedit to see it in the volume if
you want.
cheers,
Bruce
On Wed, 8 Jul 2009, Barnali Basu wrote:
Thanks Bru
Thanks Bruce. How do I figure out where it should be in the volume based on
?h.white.surface ?
On Wed, Jul 8, 2009 at 3:53 PM, Bruce Fischl wrote:
> Hi Barnali,
>
> it won't matter. If you run the subject through recon-all you can either
> draw the label on the inflated surface, in which case w
Hi Barnali,
it won't matter. If you run the subject through recon-all you can either
draw the label on the inflated surface, in which case we will
automatically figure out where it should be in the volume (based on the
?h.white surface), or you can draw it directly in the volume. The surface
what is noise0.5_0? It isn't a surface file given the output of
mris_euler_number. Try running
mris_euler_number rh.orig
On Thu, 9 Jul 2009, Feng-Xian wrote:
Hi,
Thank you for your response! But, I canÿÿt find vertices number of a
surface through typing the following command:
mris_euler_numb
Hi Natalia,
does the label line up in the volume when viewed with tkmedit? How are you
mapping it into standard coords? Are you using mri_label2label?
cheers,
Bruce
On Wed, 8 Jul 2009, Natalia Sanchez wrote:
Hi FreeSurfer experts!
I am kind of new to FreeSurfer and this is my first time us
Use mris_preproc with the --cache-in option. This will generate the "y"
file used by mri_glmfit.
doug
Victoria Williams wrote:
Hello,
I was hoping to get some more information about the qcache option.
Would running all my subjects with qcache save me any time if I plan
on using mri_glmfit
not quite, just
recon-all -s subjectname -i file.mnc
doug
Jesse Bledsoe wrote:
Hi Everyone,
What is the process for reconstructing a .mnc file with freesurfer? Do
I just run the recon-all -s /.mncfile/ -autorecon-all ?
Thanks in advance,
jesse
__
Not
You can't do that with a contrast matrix. In general, you can't test
"ANDs" with a contrast, you have to test "ORs". For AND, you have to use
a conjunction in which you make two contrasts A > B and B > C, threshold
both (mri_binarize), then do a logical AND.
doug
Feng-Xian wrote:
Hi,
I wan
Hi all,
after running a group comparison using qdec I wanted to use mc-z
instead of FDR for multiple comparison correction
I tried to run mri_glmfit-sim-mc-z.abs.2
and got an error...
ERROR: dimension mismatch between X and contrast /Users//subjects/
qdec/Untitled/tmp.mri_glmfit-sim-5637/
it would be -i -s -autorecon-all
cheers,
Bruce
On Wed, 8 Jul 2009, Jesse Bledsoe wrote:
Hi Everyone,
What is the process for reconstructing a .mnc file with freesurfer? Do I
just run the recon-all -s *.mncfile* -autorecon-all ?
Thanks in advance,
jesse
Hello,
I was hoping to get some more information about the qcache option. Would
running all my subjects with qcache save me any time if I plan on using
mri_glmfit instead of qdec? The GLMs I am running have to be sent through
mris_preproc and mri_surf2surf each time since some inputs are #'d
Hi,
I want to analysis three independence groups. And, I want to display a
result of A group > B group > C group with positive(red) and A group < B
group < C group with negative(blue). To show that, how do I write the number
of columns in the contrast matrix?
Thank you in advance!
Feng-X
Hi Everyone,
What is the process for reconstructing a .mnc file with freesurfer? Do I
just run the recon-all -s *.mncfile* -autorecon-all ?
Thanks in advance,
jesse
__
Note: Information contained in this electronic message and any attachments
to this messag
Sorry, looks like a copied old versions to the ftp site. I've put the
new ones there, let me know if it fixes it.
thanks
doug
Douglas N Greve wrote:
Nasim and Judith (and everyone else),
I've found and fixed a bug that was causing the surfcluster results
for the mc and perm simulations of
You probably have an older version that does not recoginze --cortex. Try
--label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead
Feng-Xian wrote:
Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the followi
Have you looked at the --help? There's quite a bit of documentation
there. Take a look and write back if you still have questions.
doug
Natalia Sanchez wrote:
Hi:
I am using mri_label2vol to create cortical regions of interest of M1.
What should I use for the template? (--temp argument?)
Th
Hi,
Thank you for your response! But, I can’t find vertices number of a
surface through typing the following command:
mris_euler_number noise0.5_0
When I type the command, the terminal shows some information as follow.
euler # = v-e+f = 2g-2: 0 - 0 + 0 = 0 --> 1 holes
F =2V-4:
Hi,
Thank you for your response! I solve this problem of mris_preproc.
The next step is to do mri_glmfit.
And, when I type the following command:
mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd
dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.no
any of the conformed volumes should be fine, since they all have the same
geometry (orig.mgz, brain.mgz, ...)
On Wed, 8 Jul 2009, Natalia Sanchez
wrote:
Hi:
I am using mri_label2vol to create cortical regions of interest of M1. What
should I use for the template? (--temp argument?)
Thank you
Hi:
I am using mri_label2vol to create cortical regions of interest of M1. What
should I use for the template? (--temp argument?)
Thank you
--
Natalia Sanchez
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Hi Paula,
these aren't defects, they are just small scale bumps that aren't quite
smoothed out. They only need manual intervention if the ?h.white and/or
?h.pial surfaces do not appear accurate in tkmedit. I think the ones you
are showing are fine, but double check the surfaces to make sure.
Hi Paula,
can you send us a snapshot? The inflated surface can have bumps in it,
which usually are not a problem. You can also inflate more using the -n
switch. From the surf dir:
mris_inflate -n 10 lh.smoothwm lh.inflated
where 10 is the default and you can increase it to get smoother surfac
sorry, can you give us more details? I don't understand what you are
trying to do
Bruce
On Tue, 7 Jul 2009, Barnali Basu wrote:
Experts,
I have some snapshots of ROIs made in BrainVoyager (in non-TAL space on
inflated brain, as well as ones projected onto TAL space).
I need to take the above
Some bumps are normal. I think you should post a screenshot.
2009/7/8, pcrai...@cc.hut.fi :
> Hello,
>
> I have run recon-all for my images but the resulting inflated surface
> has a lot of bumps on it even after first hand edits to the brainmask
> and wm volumes. I have tried manually removing
Hello,
I have run recon-all for my images but the resulting inflated surface
has a lot of bumps on it even after first hand edits to the brainmask
and wm volumes. I have tried manually removing the bumps one by one by
editing the wm volume but it did not have the effect I was hoping for.
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