Hello List,
I want to run an F-test on a ROI (I selected the voxels with some
criterion).
If I understand correctly the way to do it is by computing the F-statistic
using:
F=(roi_betas'*X'*M*X*roi_betas)/(Y'*R*Y)*(J-p)/p1
where:
roi_betas are the average beta values across the roi
X is the desig
Hi Bruce,
I've seen this brought up on the list a few times, and, I have to admit,
I've never really been able to wrap my head around it. The naive part of my
brain feel like, if fsaverage is an "average" subject, it should be smaller
than about half of subjects but also larger than about half of
Hi Nikolas,
did you see the "no space left on device" error? Is your partition full?
I can convert the orig.mgz with no problem. Also, why is the image 512^3?
That's a giant image, and at 1mm way more than you need to fit a human
head. Did you zeropad it for some reason?
cheers,
Bruce
On Wed,
It has to be float because that's what it uses internally. Can you break
the volume up into slices? If so, then you can analyze each separately
then combine the results back together (can't do correction for multiple
comparisons though).
doug
On 5/11/11 10:19 AM, Bruce Fischl wrote:
> no easy
Hi Boris
1. That's fine.
2. The surface area of fsaverage is less than any individual, so you
*definitely* don't want to use it. You should map the ROI back to
individuals and compute it in the native space.
cheers
Bruce
On Wed, 11 May 2011, Boris Bernhardt wrote:
> Hello Freesurfer-experts,
Hello Freesurfer-experts,
I just analyzed some FreeSurfer cortical thickness data that have been
surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage).
For the visualization and reporting of my findings, I have a two questions:
1. Is there anything that conceptually speaks ag
Hi,
I apologize for spamming the list, but for future reference this problem was
resolved when I opened the color table and annotation file on the average
brain in tksurfer and then exported the annotation file with a new name.
Using the new annotation file with mri_surfcluster, the color table wa
would it be possible to send me your .qdec project file? it can be
uploaded to me using our file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
and i'll see if i can replicate the problem here.
another option is to get a beta of the upcoming v5.1:
ftp://www.freesurfer.net/pub
Hello all!
I have a question regarding using freeview.
When doing a 3D rengering of t-maps, there is a setting that allows you to
view clusters with peak t scores. When we do this peak t scores are
included in two clusters. We wish to only show ONE cluster for an image
we are creating. How doe
Hi all,
I wanted to follow-up on my previous e-mail, which may have been a bit too
vague.
I am using the command:
mri_surfcluster --in ./osgm/sig.mgh --subject average --surf inflated
--annot slt --sign abs --csd ../csd/mc-z.abs-osgm.csd --sum
./osgm/summaryfile.txt --o ./osgm/cluster_peaks.o -
sure, upload a subject and we'll take a look
On Wed, 11 May 2011, Victor Yee
wrote:
> Hello,
>
> We have some signal dropout at the top of the brain in some scans, possibly
> similar to Rutvik Desai's 02/18/10 post. However, in our case, FreeSurfer is
> not including any of the regions affected b
Hello,
We have some signal dropout at the top of the brain in some scans, possibly
similar to Rutvik Desai's 02/18/10 post. However, in our case, FreeSurfer is
not including any of the regions affected by the dropout in both its
subcortical segmentation and cortical parcellation. Instead, FreeSurf
ok. our powerpc machine is still chugging away, so we can continue to
build and distribute that platform. probably we may not support
freeview, as that involves some complicated work to get working, but the
main stream and the tools you mention can be supported.
n.
On Wed, 2011-05-11 at 10:54
We still have here an old, but very good dual-core PPC that we use to
work with tksurfer, tkmedit, qdec, glmfit and other utilities. If not at
all hard to compile, it would be good to continue having FreeSurfer
available... At some point we'll inevitably have to turn that machine
off, but it co
no easy one that springs to mind, sorry. Doug: any ideas?
Bruce
On Wed, 11 May
2011, Ed Gronenschild wrote:
> OK, so there's no workaround from your side?
>
> There are many empty voxels in the volumes,
> so as a workaround I'm going to crop the volumes
> and hope that they will fit in the 2GB.
Hi,
A while ago we were asked if still support was needed
for FreeSurfer on a PPC Mac. I was one of the "happy"
few who needed this.
But I now can inform you that as far as I'm concerned
you can discontinue this support.
Thank you for all your support sofar.
Ed
_
Hi Nick,
I´m using mac 10.6.7 and freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0
am not sure why the error comes, i have the access to read write and
execute the files/folders.
On Tue, May 10, 2011 at 7:27 PM, Nick Schmansky
wrote:
> natalia,
>
> i'm not able to replicate this error, that is, i
OK, so there's no workaround from your side?
There are many empty voxels in the volumes,
so as a workaround I'm going to crop the volumes
and hope that they will fit in the 2GB.
On 11 May 2011, at 15:51, Bruce Fischl wrote:
> oh, yes, that's definitely not enough:
>
> 4*256*256*256*72/(1024*10
oh, yes, that's definitely not enough:
4*256*256*256*72/(1024*1024)
ans =
4608
>>
On Wed, 11 May 2011, Ed Gronenschild
wrote:
> I did.
> However, without any other concurrent process
> running I get exactly the same problem. I guess
> that this is due to the 2GB limit which can be
>
I did.
However, without any other concurrent process
running I get exactly the same problem. I guess
that this is due to the 2GB limit which can be
allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
> do you have other stuff running?
>
> On Wed, 11 May 2011, Ed Gronensc
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
> 16 GB
>
> On 11 May 2011, at 15:24, Bruce Fischl wrote:
>
>> Hi Ed,
>>
>> how much RAM do you have in your machine?
>> Bruce
>>
>>
>> On Wed, 11 May 2011, Ed
>> Gronenschild wrote:
>>
>>> Hi,
>>>
>>> We are on a I
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
> Hi Ed,
>
> how much RAM do you have in your machine?
> Bruce
>
>
> On Wed, 11 May 2011, Ed
> Gronenschild wrote:
>
>> Hi,
>>
>> We are on a Intel Mac and are facing a memory problem with
>> mri_glmfit.
>> We want to apply it to a 4D volume c
Hi Ed,
how much RAM do you have in your machine?
Bruce
On Wed, 11 May 2011, Ed
Gronenschild wrote:
> Hi,
>
> We are on a Intel Mac and are facing a memory problem with mri_glmfit.
> We want to apply it to a 4D volume consisting of 72 3D volumes
> of 256 * 256 * 256 voxels each, with 1 byte pe
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit.
We want to apply it to a 4D volume consisting of 72 3D volumes
of 256 * 256 * 256 voxels each, with 1 byte per voxel. During
processing we get the error message that it could not allocate
262144 bytes for the 9313th slice.
Hi Heidi,
you should be able to make a label of the regions you want to include,
then use
% mask_label
at the tksurfer tcl prompt to remove everything else.
cheers
Bruce
On Wed, 11 May 2011,
Jacobs H (NP) wrote:
> Hi FreeSurfers,
>
> This is more a visualization question.
> I did the cortic
Hi all.
I have two subjects where the mri_nu_correct.mni in the autorecon1 step is
aborting:
$Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt floa
Hi FreeSurfers,
This is more a visualization question.
I did the cortical thickness analyses on my data and compared my two groups
statistically.
After that I ran the mri_glmfit-sim to correct for multiple comparisons using
the cluster correction.
When I visualize the results, each cluster has i
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