--
Dott.ssa Valentina Ciullo
Laboratorio di Neuropsichiatria
Dipartimento di Neurologia Clinica e Comportamentale
IRCCS Fondazione Santa Lucia
via Ardeatina 306 - 00179 Roma
Tel. +39(0)651501101
Fax +39 (0)6 90280774
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Dear Freesurfer experts,
Using tksurfer I open an inflated surface and I display the pial surface.
Then I load an overlay but I'm not able to see it correctly. Is it possible
to put a transparency/opacity value for the surface so I can see better my
overlay ?
Thank you for your help
Arnaud Bore
Hi,
I just run my first asegstats2table in version 5.3 of FS. Is not eTIV
included in the generated file anymore?
I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but,
is it any way to get the values for all my subjects in a text file as
asegstas2table does?
Thanks a
Hmmm, not sure what to say. CAn you send me
$FREESURFER_HOME/fsfast/bin/preproc-sess ?
On 10/01/2013 07:45 AM, Leila Reddy wrote:
Hi Doug,
I don't think that could have happened as I only found out about the
no-subcort-mask option yesterday (after I had done all the original
It should still be there. I changed the name to
EstimatedTotalIntraCranialVol, eg the line now looks like
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total
Intracranial Volume, 1509814.835086, mm^3
On 10/01/2013 10:50 AM, Daniel Ferreira wrote:
Hi,
I just run my first
Hi Doug,
Here it is.
cheers,
Leila
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Leila Reddy le...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 1, 2013 5:53 PM
Subject: Re: Question about
Hi Arnaud
why would transparency help? You should be able to view the overlay on
any surface without transparency (the overlay defines the colors
displayed on the surface). Can you explain further why the normal display
in tksurfer doesn't do what you want?
cheers
Bruce
On Tue, 1 Oct
Simply to make sure,
1) Is there no way that one can edit two volumes simultaneously similarly to
tkmedits aux+main volume brush?
2) When editing voxels in freeview, is there anyway to have the cursor behave
the same way it does in navigation mode. That is, I'd like to be able to see
exactly
I have to say that I'm stumped. Do you really need to resolve this
question?
doug
On 10/01/2013 12:27 PM, Leila Reddy wrote:
Hi Doug,
Here it is.
cheers,
Leila
*From:* Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a
problem with the visualization tools you are using. Have you contacted
the developers? I think the data are fine and the information in the
header is sufficient for a visualization tool to orient it properly (as
freeview
Hi Jon,
1) No, there is no way to do that in freeview.
2) In Editing mode, you can use shift+ctrl+Left mouse button to move the
cursor.
Ruopeng
On 10/01/2013 12:50 PM, Jonathan Holt wrote:
Simply to make sure,
1) Is there no way that one can edit two volumes simultaneously similarly to
Hi Doug,
it would be great if you could give me some further advise on the group
analysis of functional connectivity maps.
Specifically, I am trying to get PCC maps for certain seeds, and am not
planning any comparison between groups.
Following your previous advise, I am running isxconcat-sess
Hi Doug,
Now that I know that I wasn't inadvertently making a stupid mistake in my
analysis, and I also know how to get around the problem, I don't really need to
solve it anymore.
Thanks for your time.
Leila
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi,
Is there a way to see both side of the activation with a brain which looks
like the pial ? Without inflated maybe I'm not really familiar with
tksurfer.
So far I used tksurfer fsaverage6 lh inflated by default.
Thank you.
Arnaud
2013/10/1 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi
Dear All,
Can I co-register SWI with FLAIR images using Freesurfer?
thanks
Ayaz
The information contained in this message and any attachments is intended only
for the use of the individual or entity to which it is addressed, and may
contain information that is PRIVILEGED, CONFIDENTIAL, and
yes, bbregister should do this just fine with T2 contrast specified
cheers
Bruce
On Tue,
1 Oct 2013, Ayaz, Muhammad wrote:
Dear All,
Can I co-register SWI with FLAIR images using Freesurfer?
thanks
Ayaz
Hi, there,
I am running the hippocampal subfield segmentation on a high resolution T2 data
that only covers the bilateral hippocampus and nearby temporal lobe areas.
Following the instruction on this webpage:
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
I used the
Hi Irene,
two things:
1. Can you please send us the log files of the recon?
2. The command you executed will compute the subfield segmentation based
only on the T1, not the high-res T2.
Cheers,
/Eugenio
On 10/01/2013 04:30 PM, Irene Lee wrote:
Hi, there,
I am running the hippocampal subfield
On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
it would be great if you could give me some further advise on the
group analysis of functional connectivity maps.
Specifically, I am trying to get PCC maps for certain seeds, and am
not planning any comparison between groups.
I'm not sure I understand what you mean by that. Your inflated brain
just needs to be inflated a little more to get the folds out of it. I
cannot tell whether this is sufficient or not. I found that I had to
iterate many times (on the order of 30) to get stable results. This is
quite
Hi Doug,
Just checking again, because I haven't heard from you. So the purpose is to use
mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure
about the correct register.dat to use. The mni152.register.dat is for MNI305 -
MNI152 though.
I'm assuming that there exists
The way the software is set up, you should use mni152.register.dat with
mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces
doug
On 10/01/2013 05:49 PM, Yang, Daniel wrote:
Hi Doug,
Just checking again, because I haven't heard from you. So the purpose
is to use
If you are using mri_glmfit, just set up contrasts to test each
individual slope vs zero.
doug
On 09/27/2013 12:04 PM, Jacobs H (NP) wrote:
Hi Freesurfers,
I just looked at my cortical thickness results, in which I performed an
interaction between group (2 groups) and cognition
Hi Doug,
I understand. But the end product turned out to be a much smaller brain … so I
thought there is something wrong. What should I do here?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 10/1/13 6:00 PM, Douglas
I don't understand what you mean by a much smaller brain. Can you
elaborate?
On 10/01/2013 06:10 PM, Yang, Daniel wrote:
Hi Doug,
I understand. But the end product turned out to be a much smaller
brain … so I thought there is something wrong. What should I do here?
Thanks!
Daniel
--
Dear FreeSurfer Experts,
Is there a program that can automatically judge whether a mgh is in the rh or
lh?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
Freesurfer mailing
I thinkyou just need to change the aparc to be either transparent or
outline.
On 10/01/2013 07:44 PM, Yang, Daniel wrote:
Hi Doug,
I think I find out where the problem is. Actually the mri_vol2surf
works nicely (and it's also true that tksurfer with -mni152reg samples
the overlay to the
Not really. If this is an individual subject, you can look at the number
of vertices and see whether it matches lh or rh. For fsaverage, the
number of vertices is the same for lh and rh.
On 10/01/2013 07:45 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Is there a program that can
Hi Doug,
except Paul was saying the mni305.cor.mgz does not show up correctly
in freeview as well. Doesn't freeview handle header orientation
information properly?
--Thomas
On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Hi Paul, IMHO this is not a problem with
Hi Thomas, it loads properly for me.
doug
On 10/01/2013 08:21 PM, Thomas Yeo wrote:
Hi Doug,
except Paul was saying the mni305.cor.mgz does not show up correctly
in freeview as well. Doesn't freeview handle header orientation
information properly?
--Thomas
On Wed, Oct 2, 2013 at 1:05 AM,
Dear All,
Brainhack 2013 will be taking place in just under a month outside of Paris,
France. A welcome reception will be held on the evening of October 23rd to
be followed by the hackathon on October 24th, 25th, and 26th.
Brainhack 2013 will be highlighted by Ignite talks by:
- *Yves
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