Thank you Martin!
For only one group, would the design matrix be the same but
intercept=Group=all ones?
Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei + ß7*ICVi+ b
1i + b2i*tij + eij
Regards,
Yolanda
2013/5/28 Martin Reuter mreu...@nmr.mgh.harvard.edu
Hi Yolanda,
since
Applications are invited for a funded Post-Doctoral position in the newly
established Brain and Language Lab at the Department of Clinical Neuroscience
at the University of Geneva, in collaboration with the Swiss Institute of
Technology (EPFL) in Lausanne, Switzerland. Projects will include
For only one group you don't need a group variable. you'd drop beta 3 and 4
terms.
Yolanda Vives yvi...@pic.es wrote:
Thank you Martin!
For only one group, would the design matrix be the same but
intercept=Group=all ones?
Yij = ß1 + ß2*tij +ß3*Group + ß4*Group *tij + ß5*Genderi + ß6*Agei +
Hi Sophie
I'm not sure there's an easy way as those weren't made entirely within
freesurfer. I guess you could create a label of all positive curvature and
use the outline mode to show multiple labels
Bruce
On Wed, 29
May 2013, Sophie Maingault wrote:
Hi FreeSufer Experts,
I would
I mean; if you devide the number of vertices by the area per
aparc-parcellation, some parcellations have relatively more vertices per
mm^2 as others. If you now would compute the average thickness in for
example the lobe-parcellation, the thicknesses of some areas (the
parcellations with
I think it depends on how you do the computation. You would probably
weight each vertex by the area then sum then divide by the total area
and this is probably not much different than just averaging over
vertices without taking the area into account.
doug
On 5/29/13 9:16 AM, Martijn
sorry, I've never used SUMA. Maybe Ziad can chime in (though he's
probably never used FSFAST!)
doug
On 5/28/13 8:57 PM, Joseph Dien wrote:
I was wondering if someone could give me a summary as to how SUMA and
FSFAST differ? In other words, user interface aside, what would be
reasons to
fmcpr.mcdat are the motion estimates (mm and degrees). mcprextreg is the
motion correction parameters after analysis using a PCA, which is why
there is such a huge difference. By default we use the top 4 components.
doug
On 5/28/13 8:28 PM, Joseph Dien wrote:
I have a follow-up question for
Hi FreeSurfers,
I have a more statistical question:
I have three groups of subjects and I want to examine the effect of a
continuous variable (cognition). Is it possible to examine three groups? Or
should I do pairwise comparisons?
What would the contrast than look like? Something like this:
Hi Doug,
Thanks for the answer. How can I examine differences between the groups?
Best
Heidi
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Verzonden: woensdag 29
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights from a cluster identified with
FS-Fast in order to compute percentage signal change.
1) I see a file called beta.nii.gz that appears to have the beta
weight information. It has a four dimensional
If you want to look for an interaction between your cog score and group,
then use the following contrast:
0 0 0 0 0 0 1 -1 0
0 0 0 0 0 0 1 0 -1
This is an F-contrast with two rows
doug
On 05/29/2013 11:33 AM, Jacobs H (NP) wrote:
Hi Doug,
Thanks for the answer. How can I examine differences
Thanks Ziad, looks like it is similar to FSFAST.
doug
On 05/29/2013 11:50 AM, Ziad Saad wrote:
Hi Joe,
As Doug guessed, I never used FSFAST so I can't really tell you much
about how they differ.
SUMA will require you use FreeSurfer to create the surfaces and warp
them to standard
Just a question about the Tools -- Reposition Surface... feature in Freeview.
Is that up and running? Is there any accompanying documentation? Thanks.
-Derin
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Freesurfer@nmr.mgh.harvard.edu
The script mri_deface which is called by recon-all with the -deface flag,
requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that
Bruce and Sebastian thank you very much.
I have checked the files but they are all wrong.
These are the image info:
data_type FLOAT32dim1 280dim2 240dim3
240dim4 1datatype 16pixdim10.584741pixdim2
1.041269pixdim3
I apologize. This is the correct info:data_type INT16dim1
280dim2 240dim3 240dim4 1datatype 4pixdim1
0.584741pixdim21.041269pixdim31.041269pixdim4
0.00cal_max0.cal_min
I usually use this little bash script (named myrecon) to process my
images.
#!/bin/bash
mkdir ~/freesurfer/subjects/$1/mri/orig -p
cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/
recon-all -all -s $1 -cw256 -hippo-subfields -qcache
With this script I get the entire -all
Hi Steve
I think recon-all -deface only creates the orig_defaced.mgz which you can
then use with mri_mask to remove facial features from whatever volumes you
want.
I don't have write permissions to that directory, but I'll see if I can get
help to copy it.
cheers
Bruce
On Wed, 29 May 2013,
Hi Tina
Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote:
Hello freesurfers,
I am trying to create a figure similar to the Hagmann et al 2008 paper with
998 rois overlaid onto the surface, however, I am finding that
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
Hi Tina
Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon
hmmm, I haven't run that code in a long time. Are the colors different
but not visually so? That is, do the rgb values differ by 1 or 2 or
something like that? Or are they actualy identical?
On Thu, 30 May 2013, Tina Jeon wrote:
Yes same result as with freeview.
Sent from my iPhone
On May
On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights from a cluster identified with
FS-Fast in order to compute percentage signal change.
1) I see a file called beta.nii.gz
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