Hi Bruce (and Jorge),
Yes, it's the wm surface. I have also done the analyses with the pial
surface and the results are similar to wm surface.
To your second question: White matter volume increased over this time
period (lme analysis; controls: logP = 8.49, patients: logP = 6.34).
Since the
Hi Bruce and FS group,
Thanks again for the speedy replies and help with everything. Quick
question about editing voxels (specifically those in the lh/rh insula).
Should I simply add specific voxels to the aparc+aseg for this step? It was
a little unclear on the wiki.
Also, is there a specific
I am conducting cortical thickness analyses between hundreds of individuals
for a study we are conducting. I was getting this error
Unrecognized sub-option flag 'annot_outline'. and so I tried to do the
group analysis tutorial and input the command from the end of it (please
see command below)
Dear all,
I would like to work with the pial surfaces of my database and more
particularly with a point-to-point correspondance between each subject. But
I didn't find how to do that, only for longitudinal analysis of a single
subject which I am not interested.
Thanks in advance for you help,
Hi Lars
yes, it seems plausible, particularly since it is so universal.
cheers
Bruce
On Wed, 29
Oct 2014, Lars M. Rimol wrote:
Hi Bruce (and Jorge),
Yes, it's the wm surface. I have also done the analyses with the pial
surface and the results are similar to wm surface.
To your second
Hi Adam
sorry, I've lost the context for this. Why are you adding voxels to the
aparc+aseg in the insula?
cheers
Bruce
On Wed, 29 Oct 2014, Adam Mezher wrote:
Hi Bruce and FS group,
Thanks again for the speedy replies and help with everything. Quick question
about editing voxels
Hi Alexandre
can you tell us what you want to do with the point-to-point
correspondence? We don't usually map surfaces into a common space since
we want to have uniform resolution/sampling in the individual coords.
cheers
Bruce
On Wed, 29 Oct 2014, Alexandre Routier wrote:
Dear all,
I
Hello Bruce,
I would like to build an atlas of subcortical structures and pial surface
on my population of study. But given the anatomical complexity of the pial
surface (and the number of points), I would like to use point-to-point
correspondence so as to have a L^2 metric (I use another metric
I'm not sure what you mean by working with the pial surfaces with
respect to point-to-point correspondence. Can you give more info?
doug
On 10/29/2014 06:29 AM, Alexandre Routier wrote:
Dear all,
I would like to work with the pial surfaces of my database and more
particularly with a
What I wanted to say is that there is the exact number of points of the
pial surface for each subject and if I look to the i-th vertex of the pial
surface of a given subject, it should be located on the same area for
another subject.
Alexandre
2014-10-29 15:25 GMT+01:00 Douglas N Greve
Create a voxel shift map using epidewarp.fsl (only the shift map is
needed, don't use this to dewarp the data). Save this in
bold/b0dcmap.nii (or nii.gz). When you run preproc-sess and
mkanalysis-sess add -b0dc (stands for B0 distortion correction).
doug
On 10/28/2014 01:14 PM, B V wrote:
This is not something we support.
On 10/29/2014 10:32 AM, Alexandre Routier wrote:
What I wanted to say is that there is the exact number of points of
the pial surface for each subject and if I look to the i-th vertex of
the pial surface of a given subject, it should be located on the same
Hi Lars,
two thoughts that came up reading this thread:
- each vertex has usually more than 3 triangles (your first mail), the
number differs depending on where you are. With a uniform mesh you'd
have nearly 60 degree angles so you'd have approx 6 triangles at a vertex.
- wm volume can
Oh, okay. I thought this kind of data could be obtained since it exists for
longitudinal analysis.
Thanks for your answer anyway!
2014-10-29 15:35 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:
This is not something we support.
On 10/29/2014 10:32 AM, Alexandre Routier wrote:
What I
you can just compute the jacobian of the ?h.sphere.reg for deformation. I'm
not sure I understand how you would use an L2 metric. There are tools in
AFNI/SUMA for converting a freesurfer surface to a standard mesh that you
could use
cheers
Bruce
On Wed, 29 Oct 2014, Alexandre Routier wrote:
no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in.
cheers
Bruce
On
Wed, 29 Oct 2014, Douglas N Greve wrote:
This is not something we support.
On 10/29/2014 10:32 AM, Alexandre Routier wrote:
What I wanted to say is that there is the exact number of points of
the pial
Our usual method for electrode localization remains in the patient's space:
co-register post-op MR and CT with pre-op MR brainmask (our reference
space) and snap electrodes to patient's outer pial surface.
My idea was: register the patient's (crappy) brainmask volume to the
Talairach fsaverage
have you tried using bbregister to register post-op MRI with the pre-op
surfaces?
On Wed, 29 Oct 2014, Pierre Mégevand wrote:
Our usual method for electrode localization remains in the patient's space:
co-register post-op MR and CT with pre-op MR brainmask (our reference space)
and snap
Hi Marie -
Thanks for your response. After sending my email I found the hemisphere
average values, but the values at each vertex and in each ROI will be very
helpful!
I tried the command you provided in tkmedit and it looks perfect - thanks!
But when I try what I think is the corresponding
Okay, thanks for the answer, I'll have a look on this software.
Alexandre
2014-10-29 16:05 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
no, but I think SUMA does. Check it out. I'll cc Ziad so he can chime in.
cheers
Bruce
On
Wed, 29 Oct 2014, Douglas N Greve wrote:
This is not
Unfortunately, our pre-implant MR was acquired with double-dose gadolinium
and we can't seem to extract the pial surface from it.
have you tried using bbregister to register post-op MRI with the pre-op
surfaces?
On Wed, 29 Oct 2014, Pierre M?gevand wrote:
Our usual method for electrode
Hi Maria,
I have to say that I rarely use freeview, I prefer tkmedit and tksurfer that I
know better. So I didn't realize that the images were shifted, I guess it's
some preference in how to read the surface. I just tried and have the same kind
of shift when using freeview, so I don't think
Professor Jill Goldstein is recruiting a postdoctoral fellow with expertise
in affective or cognitive neuroscience to join her lab, the CNL-SD (
http://cnl-sd.bwh.harvard.edu)
*Job Description*
This position requires the individual to have expertise in functional
MRI. Experience
with
Hi,
I want to do source localization on 128-channel EEG. For that, I need to
create 3-layer head models for our subjects. However, our current MRI
protocol only includes MPRAGE.
I've talked with the (f)MRI team on our project about adding a single FLASH
scan in their protocol. They are mainly
That is not what Bruce is suggesting. Try to register the post-op to the
pre-op using bbregister. You can then map the pre-op surfaces to the
post-op brain
On 10/29/2014 01:58 PM, Pierre Mégevand wrote:
Unfortunately, our pre-implant MR was acquired with double-dose
gadolinium and we can't
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply. unfortunatey I still get the same error. Here is
the terminal output. Is there anything else I can do?
Hello my names Rich. I am working on a project that involves creating 3D
models of patient brains and placing ECoG (Electrocorticography) leads on
these models. I have intra-operative pictures of the leads placed on the
subjects and I'm using these pictures to attempt to accurately place the
Hello,
I am trying to obtain estimates for the local gyrification index (LGI) using
Freesurfer. I have tried to compute LGI via two different commands...
mris_compute_lgi --i lh.pial and recon-all -lgi -s subjectName. Both of
these return the same error after running for a while...
Thanks! Best, B
On Wed, Oct 29, 2014 at 10:34 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Create a voxel shift map using epidewarp.fsl (only the shift map is
needed, don't use this to dewarp the data). Save this in
bold/b0dcmap.nii (or nii.gz). When you run preproc-sess and
Dear Freesurfer Mailing list,
I have been attempting to run mri_glmfit using a complicated fsgd file
(1 categorical varible with 5 levels, 3 categorical variables with 2
levels, age as covariate). When I run the command, I receive the
following error:
gdfReadHeader: reading
Hi Bruce,
Sorry for not clarifying. A number of subjects in our set have underestimated
insula (usually anatomical right insula but sometimes both). I just uploaded an
example to the ftp.
I don’t think control points or wm edits can help with some of these so I
wanted to see how we could go
Hi Rich,
Do you have a post-operative CT scan of your ECoG patient? If you have that
and a high-res T1, you can get very accurate reconstruction of electrode
positions on the brain surface by corregistering the two.
-zack
On Wed, Oct 29, 2014 at 3:32 PM, rwlod...@uic.edu rwlod...@uic.edu wrote:
I have some post-op CT's for some of my patients but not all, do you have
a link or could you explain how to coregister so I can do it for the ones
I have? Thank you!
On Wed, October 29, 2014 9:18 pm, Zachary Greenberg wrote:
Hi Rich,
Do you have a post-operative CT scan of your ECoG patient?
Rich,
You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and
freesurfer.
First run recon-all on the patients T1 (after acpc aligning in Spm). Then
take the resultant orig.mgz file (convert to .nii using mri_convert
orig.mgz orig.nii), and corregister the post-op CT to it
Thank you so much! This will take me some time, but i'll get back to you
when I get that far.
On Wed, October 29, 2014 9:47 pm, Zachary Greenberg wrote:
Rich,
You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab,
and
freesurfer.
First run recon-all on the patients T1
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