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
> Hi Yolanda,
>
> since you have the intercept y
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 th
For only one group you don't need a group variable. you'd drop beta 3 and 4
terms.
Yolanda Vives 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 +
>ß7*ICVi+
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 like
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 relatively
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 Steenwij
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 use
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'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 couldn't
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:
0
Hi Heidi, That will test the effect of the continuous variable averaged
over the 3 groups.
doug
On 05/29/2013 10:40 AM, Jacobs H (NP) wrote:
> 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
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 m
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 str
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 differenc
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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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
lo
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
1.041269pixdim31.0
I apologize. This is the correct info:data_type INT16dim1
280dim2 240dim3 240dim4 1datatype 4pixdim1
0.584741pixdim21.041269pixdim31.041269pixdim4
0.00cal_max0.cal_min0.fi
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 pipeline
I don't understand. Did you look at the defects in tksurfer? Or the aseg?
You need to go through the processing steps and identify what failed
Bruce
On Thu,
30 May 2013, std...@virgilio.it wrote:
Bruce and Sebastian thank you very much.
I have checked the files but they are all wrong.
These
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 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 there is no
> random, u
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, "Bruce Fischl"
mailto: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
mailto:tina.j...@utsouthwestern.edu>> wrote:
Hello frees
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 2
On May 29, 2013, at 11:40 AM, Douglas N Greve 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 that appears to
On 5/29/13 10:42 PM, Joseph Dien wrote:
On May 29, 2013, at 11:40 AM, Douglas N Greve
mailto: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 signa
Tina, what version of FS are you using? At one point I fixed a bug that
caused the color to be non-unique, but I don't think the problem looked
that bad. If this is the program I fixed, then I'm pretty sure that it
would have been in by 5.2.
doug
On 5/29/13 9:01 PM, Bruce Fischl wrote:
hmmm,
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