Dear Doug,
unfortunately, I don't know how to define the source (EPI) and target
(smoothwm) within the mri_surf2surf command to apply smoothing on the FEAT
functional data.
My aim is to apply smoothing of the FEAT functional data AFTER being resampled
to the smoothwm (to avoid deficient
Did you look at the documentation by running it with --help? The sval is
the result of mri_vol2surf. Don't use the smoothwm. It will
automatically use the white surface to compute the fwhm which is what
you want.
On 6/18/14 11:09 AM, Milde, Christopher wrote:
Dear Doug,
unfortunately, I
Dear list,
One Researcher/postdoc position is available in our group at Karolinska
Institutet in Stockholm.
Application Deadline is June the 30th 2014.
--- Group and Project ---
Karolinska Institutet Center of Neurodevelopmental Disorders (KIND)
http://ki.se/kind
KIND is an excellence center
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject domain to do connectivity analyses. While
my process works very well for the Yeo networks I'm rather unsatisfied by
the results of the Choi translations.
I'm hoping
Hi Paul
Thomas Yeo (ccd) would be the best person to help you, but he may not be
reading email for a while
cheers
Bruce
On Wed, 18 Jun 2014, Paul Beach wrote:
Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of
Yeo and Choi to original subject
Hi Jorge,
Thank you for your reply!
Again considering the same model from before
intercept(random effect) + centered age + group + group x centered age
+ sex
I think what is confusing me is that I think of the [centered age]
covariate as a column vector which will contain the centered age
Hello Freesurfer experts,
I want to project a label from a volume on a decimated surface.
Normally I do something like this to generate a label from the volume:
mri_vol2surf --src subjects/foobar/mri/aparc+aseg.mgz --regheader foobar
--hemi lh --surf pial --out test.mgh
mri_cor2label --i
Hi Wang
what is the overlay? That is what must be giving the crazy values
Bruce
On Wed, 18
Jun 2014, kangchengwang0...@gmail.com wrote:
Dear Bruce,
Thank you very much for your response. The area which I made label could be
seen in the figure (below). Is the reason for large number that
Hi LMR
If the interaction
term is not statistically significant then there is no evidence of
the existence of two different groups in your sample (as far as the
longitudinal trajectory is concerned they are all controls, the
groups might be different at baseline though). This is why main
Hi Bruce,
Thanks for the response.
I actually got this pipeline partly from Thomas a few months back. However,
I wasn't sure if anyone had suggestions perhaps for a recon-all based
command for going from the MNI152 1mm template-based fit to individual
subjects. The recon-all/Freesurfer inherent
Hi,
The recon-all based striatal parcellations are based on the anatomy of each particular subject, guided by a probabilistic atlas. That is inherently likely to be more accurate that just taking a set of ROIs/parcellations defined in some (non-probabilistic)
atlas and warping them to each
Dear Bruce,
The overlay was sig.mgh,which was the result of thickness between patient
and control. The line must be within the area of blue, right?
Wang Kangcheng
Faculty of Psychology, Southwest University, China
Email: kangchengwang0...@gmail.com / wangkangcheng@163.com
Address:
It certainly does seem like their are permissions issue. From your
message below, the 'rm' and 'mv' command complained about inadequate
permissions... and the recon-all.env command failed as well.
You've installed freesurfer on your Desktop folder, which is somewhat
out of the ordinary, though
Hi,
I'm using freesurfer on a mac computer, and therefore my mouse doesn't have
a right click or middle button. Is there an alternative way to make edits
in tkmedit (such as to correct voxels erroneously classified as white
matter in recon-all) without using the mouse buttons?
Thanks,
Caroline
Hello Freesurfers,
I can not tell what the link is from the Mathematical Background in
mri_glmfit . Also, why is GLM performed instead of a linear regression (OLS
or weighted LS )? I can not see how logistic, probit, etc is better.
Thank you very much!
Sincerely,
Ye
Dear Freesurfers,
I tried the following in matlab
[coords,faces] =read_surf('\subject\surf\rh.orig')
Hp = patch('vertices',coords,'faces',faces(:,[1 3 2]),...
'facecolor',[.5 .5 .5],'edgecolor','none')
camlight('headlight','infinite')
vertnormals = get(Hp,'vertexnormals');
Matlab returns
Hello,
I am running into a segfault error when trying to use tkmedit or tksufer.
I am currently running OSX 10.7.5 and have the most current version of XQuartz
installed.
Below are the contents of the .xdebug files:
.xdebug_tkmedit:
tkmedit started: Wed Jun 18 10:58:41 2014
Hello Freesurfers,
Is there a way that I can take a look at the content of the output of
mris_preproc?
Thank you very much!
Sincerely,
Ye
On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye...@gmail.com wrote:
Dear Doug,
Thank you very much!
Sincerely,
Ye
On Sun, Apr 6, 2014 at 5:32 PM,
In this case, GLM stands for General Linear Model, and not Generalized
Linear Model (although the former is a subset of the latter). See e.g.
http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models
From:
It is just a script so you can view it with any text editor
doug
On 6/18/14 7:15 PM, ye tian wrote:
Hello Freesurfers,
Is there a way that I can take a look at the content of the output of
mris_preproc?
Thank you very much!
Sincerely,
Ye
On Sun, Apr 6, 2014 at 5:33 PM, ye tian
Dear Watson,
Thank you very much!
Sincerely,
Ye
On Wed, Jun 18, 2014 at 12:36 PM, Watson, Christopher
christopher.wat...@childrens.harvard.edu wrote:
In this case, GLM stands for General Linear Model, and not Generalized
Linear Model (although the former is a subset of the latter). See
Dear Doug,
These files typically end with .mgh. I tired opening them with text editors
and them typically give a file of unreadable characters like:
@駺9窣,@!礱@ ^@$圚@萗@.?@6%@.溋@*鳣!址@+?@!编@3岰@
祺@€錊7]@@E褸%N(?錹?諕驚]Z@?蔮@0MU@'灔@+緌@2Pq@
%?@7?@*y7@ @,?y@
Hi Caroline,
On Jun 18, 2014, at 18:08 , Caroline Lewis carolineemmale...@gmail.com wrote:
Hi,
I'm using freesurfer on a mac computer, and therefore my mouse doesn't have a
right click or middle button. Is there an alternative way to make edits in
tkmedit (such as to correct voxels
no, not necessarily. The blue area is just the suprathreshold region. Are
the numbers reported in the overlay reasonable? You can email us the
sig.mgh and we'll take a look if you want (email us the label also)
On Wed, 18 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce,
The overlay was
Does anyone know of any support (i.e. articles/data) suggesting that the V1
and V2 labels automatically created in the Freesurfer pipeline, especially
when looking at surface area/gyrification, are valid to use with clinical
populations? In particular, visually deprived populations?
Thanks!
Hi Krista
I don't think we have any idea. The labels are based purely on anatomy, but
whether those areas keep their functional specification we have no idea.
let us know if you find out though!
Bruce
On Wed, 18 Jun 2014, krista kelly wrote:
Does anyone know of any support (i.e.
OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?
On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Krista
I don't
Hello,
Can you please email me the contents of your
/Application/freesurfer/build-stamp.txt file?
And also what version of OSX you are running by typing sw_vers
(without quotes) on the command line?
-Zeke
On 06/18/2014 01:02 PM, Jace Bradford King wrote:
Hello,
I am running into a
oh, sorry, I thought you wanted to look at the script itself. The .mgh
files are binary files with pixel data. You can view them with
tksurfer/freeview. You can load them with MRIread.m in matlab
On 6/18/14 8:41 PM, ye tian wrote:
Dear Doug,
These files typically end with .mgh. I tired
Our indices are zero based, and matlab is one based. That is probably the
problem
Bruce
On Jun 18, 2014, at 1:09 PM, ye tian tianye...@gmail.com wrote:
Dear Freesurfers,
I tried the following in matlab
[coords,faces] =read_surf('\subject\surf\rh.orig')
Hp =
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