Hi all,
after doing GLM analysis I'm trying to run freeview to see results, but I
get this warning:
Surface does not contain valid volume geometry information. It may not
align with volumes and other surfaces.
What's wrong?
I'm using 5.1 version.
Thanks to all.
Claudia
--
Dott.ssa Claudia
have permissions.
Any ideas?
Thanks a lot.
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di Neuropsichiatria
Dipartimento di Neurologia Clinica e Comportamentale
IRCCS Fondazione Santa Lucia
via Ardeatina 306 - 00179 Roma
Tel. +39 (0)6 51501358
Fax +39 (0
/newtemplate/surf/lh.white
ERROR: make_average_surface
Any ideas on what the problem is? Why cannot find white surface?
I'm using 5.1 version, but I got the same problem with version 5.3.
Thanks to all.
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di
/newtemplate/surf/lh.white
ERROR: make_average_surface
Any ideas on what the problem is? Why cannot find white surface?
I'm using 5.1 version, but I got the same problem with version 5.3.
Thanks to all.
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di
(76467.08 mm2) greater than the Total
Cortical Surface (65416.6 mm2).
Are there some errors in this?
Thanks a lot to all of you.
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di Neuropsichiatria
Dipartimento di Neurologia Clinica e Comportamentale
IRCCS
Dear all freesurfers,
I have manually drawn a region of interest and saved it as a label file in
the /label folder and I now want to extract mean thickness of this ROI. How
can I do it?
Thanks a lot
Claudia
--
Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
Laboratorio di
Dear Freesurfers,
we recently processed a sample of adult patients and then we reran
autorecon-2 and autorecon-3 after editing contol points, white matter and
pial surface.
We exported the asegstat table both pre and post editing, and we got
different volumes for most of the subjects.
How is that
Claudia
if you run autorecon2 you will rerun the aseg, which will use the control
points to change the subcortical intensity normalization. If you don't want
that to happen, you need to run -autorecon2-cp
cheers
Bruce
On Wed, 24 Jul 2013, Claudia Dacquino wrote:
Dear Freesurfers,we recently
running? Earlier versions reran the aseg for autorecon2-cp, but 5.3 does not
n Wed, 24 Jul 2013, Claudia Dacquino wrote:
Thanks Bruce,but I'm sure I ran autorecon2-cp autorecon3:
recon-all -autorecon2-cp -autorecon3 -subjid.
However, is it ok to use aseg values post editing even if they look
Hi freesurfers,
I'm trying downloading the tutorial dataset but after several attempts I
still couldn't connect to the server and I recived this message repeately,
even with the -c flag:
server response error, closing connection.
I'm working on Linux Centos System and using the wget command.
Thank you for your response. Would you suggest a reference I can refer to?
2013/6/4 Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu
I would probably leave out the fissure, but not the fimbria...
Cheers,
/Eugenio
On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote:
Hi guys!
I
Hi everyone,
I'm sorry, this is a probably very basic question, but I'm a little bit
confused about the recon-all correct flowchart.
I mean, the first step is
recon-all -s subjid -all (comprising autorecon1, autorecon2 and
autorecon3), correct?
After this step if I want to add control points
everything the autorecon2-wm and autorecon2-pial would and more,
so you can just run that.
cheers
Bruce
On Wed, 5 Jun 2013, Claudia Dacquino wrote:
Hi everyone,I'm sorry, this is a probably very basic question, but I'm a
little bit confused about the recon-all correct flowchart.
I mean
Hi guys!
I have a dataset including hippocampal subfields obtained through the
-hippo-subfields flag. I want to have a measure of total hippo volume and
I'm not sure which structures should I include in the sum. I was thinking
to exclude fimbria and fissure and sum the others. Am I right? Or
Is this the problem? Is there an incorrect command?
Thanks.
Cheers
Claudia
Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
Hi Claudia
there is no autorecon3-cp, just autorecon2-cp
cheers
Bruce
On Mon, 3 Jun 2013, Claudia Dacquino wrote:
Hi Freesurfers,
I did autorecon3-cp
Ok.
Thanks a lot!
Cheers
Claudia
Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
yes, you should be running
recon-all -autorecon2-cp
cheers
Bruce
On Mon, 3 Jun 2013, Claudia Dacquino wrote:
Is this the problem? Is there an incorrect command?
Thanks.Cheers
Claudia
Il
Hi Freesurfers,
I'm trying to remove some dura which affect my surfaces with the command
recon-all -skullstrip -clean-bm -gcut -subjid
but then I can't use tkmedit to check that.
The message I get is:
Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical
volume. Tkmedit
-0. 1. -0. 128.4031
0. 0. 0. 1.
Cheers
2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com
Yes I did run mri_info, these are the results:
Volume information for brainmask.gcuts.mgz
type: MGH
dimensions: 256
yes I did answer again to the list.
no it is no full at all.
2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu
is your disk partition full? And please cc the list so others can answer
Bruce
On Thu, 30 May 2013, Claudia Dacquino wrote:
Yes I did run mri_info, these are the results
and my freesurfer version is 5.1.
2013/5/30 Claudia Dacquino claudia.dacqu...@gmail.com
yes I did answer again to the list.
no it is no full at all.
2013/5/30 Bruce Fischl fis...@nmr.mgh.harvard.edu
is your disk partition full? And please cc the list so others can answer
Bruce
On Thu
Hi Bruce,
I think wm.mgz it's accurate enough, but what you mean?
I'm trying to upload data, but I've problems with your server.
Cheers,
Claudia
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
Hi Bruce,
I think wm.mgz it's accurate enough, but what you mean?
I'm trying to upload data
Bruce,
no the intensity is lesser then 110 at those voxels, it's like 60-70.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
is the intensity at those voxels 110 after you have processed with
autorecon2-cp?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
The problem is that after
Yes it's my doubt too, but how can I check this?
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
then it's not rerunning the -cp. And is it really wm if it's that dark?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Bruce,no the intensity is lesser then 110 at those voxels, it's like
60
Actually it could not be WM, but I'm quite sure that there is grey matter
excluded by pial bounaries as well, how can I add that?
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
visually is the only way. Do you think it is white matter?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Yes
But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
-segmentation aseg.mgz it's labeled as white matter, could it be possible?
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
Actually it could not be WM, but I'm quite sure that there is grey matter
excluded by pial bounaries
surface is incorrect, so the first thing to do is make sure it is
right
Bruce
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
But in brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
-segmentation aseg.mgz it's labeled as white matter, could it be
possible?
2013/4/29 Claudia
I'm uploading my subjdir on FTP server.
Thanks a lot.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Claudia
if you upload your whole subject and send us some example voxel coords of
where you are looking we will take a look
Bruce
On Mon, 29 Apr 2013, Claudia Dacquino
my subjdir is on FTP server.
thanks
claudia
2013/4/29 Claudia Dacquino claudia.dacqu...@gmail.com
I'm uploading my subjdir on FTP server.
Thanks a lot.
Claudia
2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Claudia
if you upload your whole subject and send us some example voxel
is
dramatically wrong. Did you check any of the outputs (wm.mgz, filled.mgz,
lh.orig, etc...)?
cheers
Bruce
On Thu, 18 Apr 2013, Claudia Dacquino wrote:
Hi freesurfer,
my autorecon2-cp after ctrl pts edits exited with this error message:
CORRECTING DEFECT 0 (vertices=176788, convex
Hi freesurfer,
my autorecon2-cp after ctrl pts edits exited with this error message:
CORRECTING DEFECT 0 (vertices=176788, convex hull=8149)
Excessive topologic defect encountered: could not allocate -776253752 edges
for retessellation
Cannot allocate memory
Could anyone help me with this,
I was trying, but the administrator did reject that, because the file is
too big.
2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com
I was trying, but the administrator did reject that, because the file is
too big.
2013/3/25 Claudia Dacquino claudia.dacqu...@gmail.com
Hi Bruce,
I'll
I'm sorry, I did mean the moderator of Freesurfer mailing list.
2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu
you should be able to use our ftp site or file drop. Which administrator
do you mean?
On Mon, 25 Mar 2013, Claudia Dacquino wrote:
I was trying, but the administrator did
. You can either use our ftp site or file
drop
cheers
Bruce
On Mon, 25 Mar 2013, Claudia Dacquino wrote:
I'm sorry, I did mean the moderator of Freesurfer mailing list.
2013/3/25 Bruce Fischl fis...@nmr.mgh.harvard.edu
you should be able to use our ftp site or file drop. Which
Dear Freesurfers,
I'm new and I'm starting using Freesurfer.
I'm having a problem with one subject, during the cortical reconstruction
(recon-all) the process stops at this stage:
mri_cc http://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc -aseg
aseg.auto_noCCseg.mgz -o aseg.auto.mgz subjid
at this
Hi everyone,
I'm a very new fresurfer user and I have to understand the very simple
basis of its use yet.
So I have some maybe stupid questions about that.
I heve to work on cortical thickness, so I suppose I have to complete the
segmentation and then correcting CPs and Pial surface.
The first
interventions you can take to correct them, that
are detailed on our wiki
cheers
Bruce
On Mon, 18 Mar 2013, Claudia Dacquino wrote:
Thaks a lot Bruce,
so I have to edit WM first, and then, what about grey matter? Do I have
to paint all the None Sgmtn label points, or just
the
ones
Hi everyone,
I'm a very new fresurfer user and I have to understand the very simple
basis of its use yet.
So I have some maybe stupid questions about that.
I heve to work on cortical thickness, so I suppose I have to complete the
segmentation and then correcting CPs and Pial surface.
The first
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