Hi,
I have some problem. Could you get me some suggestion?
I get a simulation brain with no-adding noise from BrainWeb. Then, I add 1%
noise and 5% noise, respectively, to the simulation brains. When I finished
these simulation brains through FreeSurfer, I found that the cortical
thickness
That is correct. This is case of semantic dementia where left anterior
temporal region is markedly atrophic.
Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't
think that was ever the case. What pathology is this in? And y
so there's 10mm or so of gray matter with no underlying wm? I didn't
think that was ever the case. What pathology is this in? And you're sure
it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May
2009, Olivier Piguet wrote:
Hi Bruce,
In the coronal plane, slice 152 is the last slice
Sorry, I don't have anything to do this.
doug
Siddharth Srivastava wrote:
Hi everyone,
For a cluster spanning multiple labels based on a
specific annotation, is
it possible to automatically generate a list of labels (text) of the
regions it
overlaps with? What command/proce
Hi Bruce,
In the coronal plane, slice 152 is the last slice where white matter
is clearly visible. Then, slices 153-158, only grey matter is
recognised but not all of it, and slices 159-164, grey matter is not
recognised at all.
I added control points on slice 151-153 in the hope that it w
Hi Oliver,
how far away is the nearest white matter?
Bruce
On Fri, 15 May 2009, Olivier
Piguet
wrote:
Hi there,
I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When
examining the surfaces in tkmedit, the left temporal pole
Hi everyone,
For a cluster spanning multiple labels based on a
specific annotation, is
it possible to automatically generate a list of labels (text) of the regions
it
overlaps with? What command/process should do this? mri_surfcluster is just
providing me with the parcellation wh
Hi there,
I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When
examining the surfaces in tkmedit, the left temporal pole is not
included in the pial surface. Is there a way to force freesurfer to
recognise this as valid brai
Try running reg-feat2anat on your fmri data. This will register the
functional data to the subject's structure (which is not useful for this
case). But it will also compute the matrix which registers the
anatomical and mni152. This will be in
featdir/reg/freesurfer/anat2std.register.dat
Fir
also i've tried ;
//mri_convert -it dicom -ot nii /home/ozgun/AnV/dti
samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA
/home/ozgun/AnV/ok.nii /
output was;
/
$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp
$
reading from /home/ozgun/AnV/d
Hi,
I did not receive a response to this yet. Does it mean it is not possible?
Thanks!!
Vina Goghari wrote:
Hi Doug,
Yes the FSL group analysis is in MN152 and then I want map that back
to each individual's brain that were analyzed and parcellated using
FreeSurfer, so I can extract thickness
just give it one file in the series as input, and it will find the rest.
ozgun ozalay wrote:
Hi;
i have 70 Siemens .ima files in a single directory. Does anyone know how
to convert ALL files in a folder into another format using mri_convert ?
Do i have to convert them one by one?
Does "--sdcml
give it one slice from the series you want to convert
On Thu, 14 May 2009,
ozgun ozalay wrote:
Hi;
i have 70 Siemens .ima files in a single directory. Does anyone know how
to convert ALL files in a folder into another format using mri_convert ?
Do i have to convert them one by one?
Does "--s
Hi;
i have 70 Siemens .ima files in a single directory. Does anyone know how
to convert ALL files in a folder into another format using mri_convert ?
Do i have to convert them one by one?
Does "--sdcmlist" option does this?
Simple usage;
/mri_convert /
ie: mri_convert /home/ozgun/AnV/aman.im
Hi again,
I have been encountering an error when attempting to use either tksurfer or
tkmedit via VNC on a local server. Here is the output whenever I type
tkmedit or tksurfer:
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by
display: 1.0
I looked through the threads rega
You should use:
ozgun.oza...@gmail.com
7235
*CZag.N9G9Ekc
Only three lines in license file
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
2009/5/14 ozgu
Hi;
I'm Ozgun Ozalay, researcher at Ege University/Turkey. One of my friends
recommended FreeSurfer's "mri_convert" program to convert my Siemens
.IMA files to a more common format .nii.
i've downloaded freesurfer from your wiki pages and made my registration
too. i've recieved an e-mail with det
I'm working with a Stable 4 version of FreeSurfer.
I think your explaination about the vertices is acctually the answer to my
question. The variation that I'm seeing between the pre-masked, and
non-pre-masked surface is quite small, but never-the-less present. If
this is the case, I think t
What version are you using? I just checked this on my current version
(and this part has not changed in a long time), and it gave the same
result in the mask regardless of whether I masked the input or not. One
thing that I did find is that it will smooth the vertices that are
outside the mask
You are correct, surf2surf is not changing the values from out side the
masked region. However the problem is that in smoothing the values inside
the masked region surf2surf appears to be incorporating values from
outside the masked region (even if its not smoothing these "outside"
values).
To do this, you need to have the registration file between MNI152 and
the subject space. When you say subject space, do you mean the
anatomical space or functional space?
doug
Campanella Martina wrote:
Hi "Freesurfer",
We need to remap a volume in MNI152 to a subject space in
order to find
Can you send us the info requested in
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?
doug
Rodrigo Zepeda wrote:
While trying to coregister a ct.nii and a orig.mgz file using the
following command:
spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the
I was just going to average the field sign over the calcarine and
multiply all vertices by -1 if that average came up negative. I can't
remember what example made me think this was necessary. I remember
seeing changes in the sign, but I can't remember whether it was
subject-specific or if it ch
mri_surf2surf will not change the values outside of the mask (those will
be left unsmoothed). Is there an actual difference in the mask?
doug
Gregory Dierksen wrote:
Hi,
I want to smooth a cortical thickness map using values only in a
specific area. Basically I want to mask out all o
Dear all,
A Senior Lecturer Post has now opened at York University, England.
https://www22.i-grasp.com/fe/tpl_YorkUni01.asp?newms=jj&id=25711
(https://www22.i-grasp.com/fe/tpl_YorkUni01.asp?newms=jj&id=25711)
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Hi "Freesurfer",
We need to remap a volume in MNI152 to a subject space in
order to find the correspondent label...
Any suggestion?
Cheers,
Martina Campanella
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